Hodgdon Extreme

It's a straightforward calculation:
(573000 / bore diameter in mm) / 1000 = knock frequency in kHz
For you, it should be 6 kHz for the first order of resonance, or 12 kHz for the second
The issue I see with your arrangement is your sensors are super duper quiet. It should normally only take a Gain Channel of 3-5 to see a Knock Level amplitude of 200-300 or so... Yours are 2-5, so about 100 times lower than they should be.
First thing I'd do is swap the sensors out for flat-response sensors. However, the Knockblock unit comes with a pair of them - so if you're planning to buy a Knockblock anyway, you'll get the better sensors. 

I used to run dynos for the OEMs. I know of no other way to develop ignition tables other than hammering out tests on the dyno. MBT is pretty easy and can be done on a chassis dyno pretty well; but if you want to minimize pumping losses and BSFC at less than WOT the way the OEMs do - it'll need to be done on an engine dyno - or take lots of time and fuel doing it on the street empirically.
I suspect you are already well aware - but it bears repeating: be super careful reading into other internet people's ignition timing values. Did they truly get the trigger offset and ignition delay correct? Are the timing marks on their balancer even accurate? Are yours? Do they shine the timing light on the balancer and look at it from the same angle as you? There can easily be 5º or more accumulated error based on these factors.

I used to run dynos for the OEMs. I know of no other way to develop ignition tables other than hammering out tests on the dyno. MBT is pretty easy and can be done on a chassis dyno pretty well; but if you want to minimize pumping losses and BSFC at less than WOT the way the OEMs do - it'll need to be done on an engine dyno - or take lots of time and fuel doing it on the street empirically.
I suspect you are already well aware - but it bears repeating: be super careful reading into other internet people's ignition timing values. Did they truly get the trigger offset and ignition delay correct? Are the timing marks on their balancer even accurate? Are yours? Do they shine the timing light on the balancer and look at it from the same angle as you? There can easily be 5º or more accumulated error based on these factors.

I used to run dynos for the OEMs. I know of no other way to develop ignition tables other than hammering out tests on the dyno. MBT is pretty easy and can be done on a chassis dyno pretty well; but if you want to minimize pumping losses and BSFC at less than WOT the way the OEMs do - it'll need to be done on an engine dyno - or take lots of time and fuel doing it on the street empirically.
I suspect you are already well aware - but it bears repeating: be super careful reading into other internet people's ignition timing values. Did they truly get the trigger offset and ignition delay correct? Are the timing marks on their balancer even accurate? Are yours? Do they shine the timing light on the balancer and look at it from the same angle as you? There can easily be 5º or more accumulated error based on these factors.

The CAN gages on the market are pretty cool. Link sells ones that appears to be a private-labeled version of the GageArt unit. BTI sells another.
Bottom line, it can be configured to display anything the ECU is aware of. It can show one, two or four channels at a time. You can configure multiple "pages" and cycle through those pages with the touch of a button. Very nice.

The CAN gages on the market are pretty cool. Link sells ones that appears to be a private-labeled version of the GageArt unit. BTI sells another.
Bottom line, it can be configured to display anything the ECU is aware of. It can show one, two or four channels at a time. You can configure multiple "pages" and cycle through those pages with the touch of a button. Very nice.

That would suggest you are using the wrong trigger mode, possibly the multitooth/missing mode?  The correct trigger mode for this engine is "1JZ VVTi" and the offset should be near zero.   You will have unreliable sync/no start/long startup and sometimes VVT errors if you are trying to use "cam pulse 1X" sync mode with a 3 tooth cam. 

Looks like your closed loop lambda control is putting in the max-clamp amount (10%) extra fuel and yet still struggling to maintain stoich. As soon as you blip the throttle, it goes super lean - and the CLL correction disables based on your lockout conditions.
You can probably multiply your master fuel by 1.15 as a starting point to retest.
Also, if it were me, I'd give CLL more control authority - especially and/or at least while you are trying to get things in the ballpark. I'd simplify your min/max CLL control from 3D tables - and just use a simple scalar of ±20 or 25%.
Also noticed your acceleration compensation sensitivity is 10 at all engine speeds. That seems like a lot to me. I think you'll find yourself in the 4-5 zone at low RPM and 1-2 in the high RPM zone.

Obvious answer helped, thanks guys. Should've started there. Low throttle is way too toey so I'll scale it back a touch but not as much as it was previously.

Your throttle tracking looks ok to me but your target looks pretty tame, that could possibly make it feel pretty lazy.  For example at the time mark -3:12 in your pic above we cant see the actual APS as it is off the screen, but the axis goes to 23% so we can say you have more than 23% pedal commanded, but your TPS target is only 12.5%.  

I use and recommend the Belkin 5m USB active extension cable pn F3U130-16 . 

You will need an active USB extension.  I have a 10M Unitek Y-278 that I use an engine dyno that works good.  

Correct, the update rate should be more closely related to mass flow rather than RPM, in the next firmware update you have the ability to enable user configurable 3D table for update rate and gain.  
However, my policy with tuning is usually to only add complication where necessary, in my car even though I have the ability for a 3D table and I have tried it, I find just the 2D table referencing RPM is all I need.  I suspect just a 2D table with something like "Air per Cyl estimated" on the axis would be a good easy option but I havent personally tried any alternatives like that yet.
Edited the first line of this post as the 3D table comment should have only applied to the update rate, I was mistaken about the gain table.

This product makes it way easy to deal with sinusoidal signals from variable reluctance speed sensors:
https://sirhclabs.com/product/vr-to-hall-sensor-converter/
They sell a dual-channel unit also:
https://sirhclabs.com/product/vr-to-hall-sensor-converter-dual-channel/
Basically you hook up the two wires from the VR sensor, +5V power, sensor ground - and it outputs a nice clean 5V square wave. Even better, it sinks no current so you can tap into VR signals and "listen in" to them without disturbing the basic signal - which means you can leave the WSS signals hooked up to your ABS module, but also use them as inputs into your G4x.
I have this up and running on my IS300 - I have OEM ABS functional with no error codes, meanwhile I have a front WSS piped into the G4x for traction control calibration. The signal comes alive at less than 1mph.

I installed one of the big walbro pumps in my turbo IS300. It can draw 25 amps, so I chose to use a SSR so I can drive the pump only as hard as required to maintain sufficient fuel pressure. My intention was not to precisely control fuel pressure via PWM, so I have not implemented fancy duty cycle calibration maps/surfaces; just a simple 2D table of DC versus MGP so the pump increases DC as MGP increases.
Here is my system wiring diagram:

Basically I'm using the OEM relays to ultimately close a heavy duty 50A fuel pump "isolation" relay. This is because solid state relays leak current even when they're open - so the 50A relay removes power to the SSR when the key is off.
Note the fast acting flyback diode spliced across the pump power leads!

I mounted the SSR to a heat sink. I think it's overkill because it doesn't seem to get very warm.

I've got my PWM frequency set at 450Hz and it's been working great. 
I used a Crydom 100A solid state relay:

Be sure you get one designed specifically for direct current!
Here are some other potential choices for relays:

HELLA
PART NUMBER: 4RA-931-773-98 or 4RA 007 865-031
They're rated at 22A switching current which means they can handle more at 100% duty cycle. The big Walbros can draw about 25A - so I think this relay would do the job.
 

Part # 15620NOS
Rated at 20A switching and 40A continuous. I've read a bunch of good reviews about this unit.
 

Dorman 902-310 Engine Cooling Fan Relay Kit
Unsure on current rating, but fan motors draw a lot. Again, many good reviews on these.

Here's my saga with same errors
 
In the end moving the ground away from coils ground solved it for me.
 
 
 
 

For a true "rev match" you would have to use the motorsport gear shift function which is over the top for what you want I think.  
To use the gear shift function to achieve a rev match it would be done something like this:
In road car with an H pattern shift and no strain gauge or similar on the lever then really the only thing you have to indicate to the ecu that you want to initiate a gear shift is a switch on the clutch pedal.  But that alone doesnt tell the ecu whether you want to do an upshift or downshift.  So you use a GP output to asses a whole lot of conditions that you think would be present for a down shift but not an upshift.  This, for example, could be something like Throttle pedal is not pressed, clutch and brake pedal are both pressed and the speed is above 30kmh.  Whenever the ecu see's all of those conditions true then it will initiate a downshift sequence.   
Next, for the ecu to be able to rev match, it needs to know what gear you are in and the ratio of the current gear and the ratio of the next gear that you want to engage.  Since you dont have a gear position sensor, you will need a working speed sensor so the ecu can then determine which gear you are in by using speed, RPM and gear ratios. 
With all of that the ecu would then have enough info to generate an RPM target that it needs to hit with the blip based to achieve matched input and output shaft speeds during the shift.  This RPM target can be met in 3 different ways.  1). You can use a speed match limiter - this is where the ecu blips the throttle a little more than is required and introduces a rev limiter to control the RPM at the desired target.  This is the most accurate and fastest blip. But you dont really want to be bouncing on a limiter on every shift when driving around town etc. 2). You can use what we call an RPM target blip. This is where the ecu performs a blip then removes the blip once the target RPM is reached. Since the throttle doesnt close until you are already at target you will get quite a bit of overshoot with this method.  3). A predictive blip, this is where the ecu looks at the rate the engine is accelerating during the blip to predict how long it will take to reach the correct RPM, it can then close the throttle early so you dont get as much overshoot as method 2.  
Having said all that, it is rare to do a proper RPM match for a road car with a synchro gearbox, the normal technique is just to switch to a 2nd e-throttle target table when your downshift conditions are met.  That table can have RPM Vs gear or Speed Vs gear on it so you can command more blip for high speed gear changes and less or none for low RPM/speed shifts.  
 

Yes, the settings you suggest above take care of the general change in air density due to altitude. 
However there is another factor to consider with turbocharged engines - if you want to maintain the same MAP (same power) as altitude increases, then the turbo charger has to work harder due to the increasing pressure ratio (higher boost/MGP is required to maintain the same MAP), this means higher EMAP which of course reduces the engines VE. So you may need a 4D table referencing either EMAP or Altitude/BAP to correct for the restriction that the turbocharger adds at higher altitude.  

some bloke on the Subaru forums plotted a few Defi calibration curves
http://bbs.22b.com/forums/showthread.php?8223-Defi-Sensor-Calibration-Curves
 
Pressure:
0psi=.580v
5psi=.753v
10psi=.837v
15psi=.978v
20psi=1.112v
25psi=1.250v
30psi=1.392v
35psi=1.525v
40psi=1.670v
45psi=1.811v
50psi=1.954v
55psi=2.095v
60psi=2.239v
65psi=2.372v
70psi=2.504v
75psi=2.647v
80psi=2.780v
85psi=2.926v
90psi=3.063v
95psi=3.200v
100psi=3.326v
105psi=3.454v
110psi=3.596v
115psi=3.739v
120psi=3.882v
125psi=4.000v
130psi=4.150v
135psi=4.280v
140psi=4.420v

Temp:
DegC Voltage
25 = 4.548
30 = 4.481
35 = 4.402
40 = 4.3115
45 = 4.212
50 = 4.1045
55 = 3.986
60 = 3.858
65 = 3.726
70 = 3.583
75 = 3.429
80 = 3.2785
85 = 3.119
90 = 2.9625
95 = 2.8105
100 = 2.6595
105 = 2.509
110 = 2.342
115 = 2.2025
120 = 2.0575
125 = 1.9205
130 = 1.775
135 = 1.657
140 = 1.542
145 = 1.435
150 = 1.329
155 = 1.2355
160 = 1.1565
165 = 1.0755
170 = 1.0045
175 = 0.942
180 = 0.8855
185 = 0.8515
190 = 0.814
195 = 0.795
200 = 0.776

There are lots of DIY options for building your own "knock block" audio device. Essentially incorporates a knock sensor, an amplifier and a set of headphones. I built one several years ago and it worked fine - though honestly I prefer a simple pair of "det cans" - basically a stethoscope arrangement terminating to a piece of copper bolted to the engine block. Seems ridiculously simple, but extremely effective.
I've not used the Link KB unit; I assume it has fancy audio filtration that removes a lot of the background mechanical noise. Det-cans don't have that, but you learn really, really quick what actual knock sounds like.
Fun related story - back in my dyno days, we had all the top end AVL dyno equipment and software, including their super-fancy inidcom combustion analysis system with in-cylinder piezo pressure transducers... We still used the old school copper tube bolted to the block, running under the testcell door, clamped to a steel funnel mounted to the control panel.
There were plenty times the indicom system indicated knock you couldn't hear AT ALL in the funnel - and other times you could CLEARLY hear knock in the funnel - but the indicom system indicated nothing. We all trusted the copper tube/funnel (we called it the iron ear or "binford 9000") much more than that fancy system.

There are lots of DIY options for building your own "knock block" audio device. Essentially incorporates a knock sensor, an amplifier and a set of headphones. I built one several years ago and it worked fine - though honestly I prefer a simple pair of "det cans" - basically a stethoscope arrangement terminating to a piece of copper bolted to the engine block. Seems ridiculously simple, but extremely effective.
I've not used the Link KB unit; I assume it has fancy audio filtration that removes a lot of the background mechanical noise. Det-cans don't have that, but you learn really, really quick what actual knock sounds like.
Fun related story - back in my dyno days, we had all the top end AVL dyno equipment and software, including their super-fancy inidcom combustion analysis system with in-cylinder piezo pressure transducers... We still used the old school copper tube bolted to the block, running under the testcell door, clamped to a steel funnel mounted to the control panel.
There were plenty times the indicom system indicated knock you couldn't hear AT ALL in the funnel - and other times you could CLEARLY hear knock in the funnel - but the indicom system indicated nothing. We all trusted the copper tube/funnel (we called it the iron ear or "binford 9000") much more than that fancy system.