koracing

If you disconnect the wires from the ecu do you get the same voltages as are being logged by the ecu on AN volt 11? 
Doing a little quick math as I noticed AEM offers a 100psi x-series gauge as well as a 150psi, the value offsets you are reporting are almost dead on if your sensor is 100psi, and not 150psi.  Perhaps the sensor/gauge was mispackaged?
3.7v would be 120psi on the 150psi gauge, and 80psi on the 100psi gauge.
2.5v would be 75psi on the 150psi gauge, and 50psi on the 100psi gauge.
Also if you want to see a kpa input sensor in psi, you can always do the conversion on a math channel so the data would be *more* accurate - but that's probably more personal preference than anything if one isn't doing anything critical with the data.

To figure out if you need more air or fuel when cold starting: crack throttle slightly (Maybe 2-10%) while cranking cold and see if it improves, or makes it worse, or no change.  Setting up a full throttle flood clear can be useful here to clear the cylinders if you think it's over-fueling.  If none of that makes any difference, try spraying a spritz or two of starter fluid or carb cleaner into the throttle body and see if it wants to light off (artificially adding more fuel vapor).  Something here should lead you in the proper direction of if the motor is wanting more fuel or more air.

To figure out if you need more air or fuel when cold starting: crack throttle slightly (Maybe 2-10%) while cranking cold and see if it improves, or makes it worse, or no change.  Setting up a full throttle flood clear can be useful here to clear the cylinders if you think it's over-fueling.  If none of that makes any difference, try spraying a spritz or two of starter fluid or carb cleaner into the throttle body and see if it wants to light off (artificially adding more fuel vapor).  Something here should lead you in the proper direction of if the motor is wanting more fuel or more air.

Keep in mind the cranking enrichment is a percentage based on the base fuel table values, and you also have start prime, and first crank enrichment options to inject additional fuel.  I don't see any reason 870cc injectors should require 600% enrichment to fire up decently cold.  I've had 2200cc injectors fire up on 75-80% ethanol at 40°F ~ 4°C just last week without issue.  Cranking enrichment was about 250% at that temp just FYI.  Dialing in warm running and starting first may be a better way to get where you need to be as you can spend a lot more time warm to perfect starting.

There are spark testers that work great for a go between the coil packs and plug for this purpose.
https://www.summitracing.com/parts/lil-20610?seid=srese1&gclid=Cj0KCQjwspKUBhCvARIsAB2IYuubY5BMnLaTSMPSIGbTxDrAi7mZArUMIpoiCzsl8UYXEhQR2nZ96iQaAk8KEALw_wcB

One thing I recommend doing with the LTT is to try and set the axis break points to match your fuel table break points as much as possible in the regions where you want to have the LTT active.  I wish the LTT table was as large as the fuel tables, but it is not.

Reading the instructions with the AEM X-Series GPS Speedo it looks like there are two wires on connector B - A yellow and a violet wire.  The signal is listed as a 12v pulsed output so you should be able to run the signal wire to a Digital input (DI) and then ground the ground wire to the ECU sensor ground.  Then calibrate vs. a phone app or dyno roller speed.

Another good solid state relay option is the NOS 15620 relay (Nitrous Oxide Systems).  It's got good current capability, extremely low response time, and can be PWM'ed to 1000Hz.  

I typically set the table like above versus MAP instead of RPM and set it to close above 105kpa (setting base position row values at 100 and 105kpa).  I don't care too much if the IAC hangs open off boost as long as the air source is filtered.  If you're getting a huge vacuum leak - is it causing the car to hang above idle speed?  Is it just the noise you are having issue with?

Im in the middle of doing the same thing, unfortunately no someone has to manually move everything over.

To figure out base timing on a new setup I recommend removing all of the coils and spark plugs except cyl 1 and then use a piece of plug wire or a spark tester to plug the coil to an then plug onto the spark plug.  Disable injectors (unplug them) and crank with trigger scope and timing light.  If someone cranks while in trigger setup and timing fixed you should see the timing light flashing at the same value if your triggers are correct.  Also check your trigger scope versus the cranking and you'll notice with all the plugs out except cyl 1 that the spacing on the crank trigger teeth will be close together except when building pressure in cyl 1 which is when you should be about to fire.  You can count teeth between this signal and the cam sync signal to see if the offset seems close or if it's one crank revolution off as you should only see the wider spaced teeth in trig 1 once per 2 crank revolutions.  In your scope it looks like your trig 2 falling edge is about in line with the 25th tooth from the gap on your trig 1.  Your sync tooth is listed as tooth 16 and your offset is -5 so that does seem a bit far off.
Your dwell times are pretty high for those coils as well - you want to be around 1.5-2ms at 12v and higher.  I'm not sure what you set your ethrottle minimum to but you shouldn't need much more than 5% to idle and start typically.  If you set your minimum to zero and manipulate the throttle when trying to start it may allow you to figure out what exact percent throttle you need to obtain desirable starting condition and idle speed.  Of course fueling needs to be in the ballpark for this to work.
Small thing: your engine displacement is listed as 2200cc - but with a .5mm overbore 5s block (87.5mm bore) and 91mm stroke crank - your displacement is 2189cc (rounding).  

Small suggestion: Alternator control to me would seem more at home in the chassis and body rather than aux outputs?  Maybe it's just me but that's the first place I looked for it.

Tuning Gen4/Gen5 3sgtes I typically just eliminate this valve and run standard mechanically vacuum referenced fuel pressure direct to manifold.  I've tuned motors with and without it, and have seen no noticeable benefit to keeping this VSV.

I'm personally against locking out tunes - particularly if you're paying the tuner for the work.  Not much you can do without getting access to the tune at this point unless you want to start over with someone else.

Between enabling the pullup resistor and saying if Neutral/Park is active low or high, you can change which way the active state works in the software.  You should need more idle duty cycle in gear than you would in Neutral/Park.   That trim only adds 0-25%, and can't subtract it, so you should have it active while in gear (which seems counter-intuitive to the name of the trim).  
FWIW You will want to try it and see how the car reacts, however, because I wasn't able to get enough range of adjustment on an old 69 Dodge dart with a A904 automatic using that trim.  In addition to that in that application, the only way I got this to work reliably was with idle set to open loop as the closed loop would take the trim amount away after a bit and cause idle to dip or go over (can't remember which) when changing state back and forth.  I ended up just doing a 3D idle table with coolant temp on one axis and park/neutral on another axis (0 and 1 for on or off) with two rows for idle duty in gear and idle duty in neutral/park.  Idle ignition trim handled small adjustments fine to make the idle stable even with fixed idle valve duty.

Yes you can always use the software to calibrate the timing to ensure it's correct.  Marking the distributor later if you change it or remove and reinstall it should make this less work, but doesn't make it certain that the timing is correct 100% after reinstalling.  The only way to verify the timing is synchronized with the distributor and ecu is to use a timing light and calibration function in the ecu to fix the timing and ensure they match.

The TE1 and E1 jumper in the factory diagnostic port won't fix timing in the Link - you'll have to refer to the help menu to do this.  It is, however, possible to make the TE1 pin work like the OEM does request does and fix the timing at 10deg, but it require wiring modification to run to a digital input on the Link and setting up a fixed timing input request - a lot of work again, for little gain as you can also fix the timing by going through the calibration procedure outlined in the help manual.

Yes the idle control in the Link when properly tuned will try to correct for any situation that may decrease idle such as electrical load, without the use of the extra input.  Usually this isn't too much trouble in most situations, but it can under heavy load be a little less smooth than if that input were used.

The intercooler pump works correctly as is with our ECU with no modification, it is controlled by "INT".  The MTT, M+ & M- pins are only used to monitor voltage/current at the motor. 
 
Not really.  It is not a digital signal, the feedback circuit is a weird 3 wire analog signal representing motor current.  You are probably best to just set up a warning lamp for high IAT or similar. 
 
Inj 7 & 8 drives arent available on this ECU, if you wanted an extra fuel injector you would have to use the aux injection function with outputs Inj 5 and/or  6.  Charge cooler pump and oxy heater would need to be moved to different outputs.  
 
It is in the help file and manual pin functions list:

 
G4X manual has just been updated to show the full pinout.  G4+ pinouts used to only show pins that were relevant to set up.  Oil pressure switch is only connected to the dash board.  If you want to connect it to the ecu then yes, you can connect to a DI.  You would be better to use a pressure sensor however rather than a switch.  

For anyone with the disconnecting issue check your spark plugs and make sure they have resistors in them. Non-resistor plugs made the random disconnecting issue 1000x worse on my g4x. 

No, it's the same single tooth with two different magnetic pickups 180 apart in the distributor housing.


The tall magnetic pickup is the crank position, and the lower ones have a single tooth under the 24 tooth wheel that passes by them.
As far as I'm aware, Toyota used this same basic trigger setup for most vehicles with distributors from mid 80s to the late 90s.  Even the non-vvt 2JZ with COP is still a 12 tooth crank (which would be 24 tooth on a cam), with two single sync reluctors 180 deg appart off the intake cam if my memory serves me.
4AGZE trigger setup is the exact same as distributor 3SGTE -- the same offsets work great also BTW.  

No, it's the same single tooth with two different magnetic pickups 180 apart in the distributor housing.


The tall magnetic pickup is the crank position, and the lower ones have a single tooth under the 24 tooth wheel that passes by them.
As far as I'm aware, Toyota used this same basic trigger setup for most vehicles with distributors from mid 80s to the late 90s.  Even the non-vvt 2JZ with COP is still a 12 tooth crank (which would be 24 tooth on a cam), with two single sync reluctors 180 deg appart off the intake cam if my memory serves me.
4AGZE trigger setup is the exact same as distributor 3SGTE -- the same offsets work great also BTW.  

Haltech dash has configurable bitrate, they are fine on the same bus.  

CAN is a digital signal - just 0's & 1's going down the wire.  This means the ecu always receives exactly what the controller is outputting.  With an analog output the controller outputs a voltage in reference to a common (or sometimes not common!) ground. Very few wideband controllers have a differential ground completely isolated from power ground, so even if they have a dedicated analog ground, there is still an influence from load on the power/chassis ground.  Any offset between the ground the wideband is referencing compared to the ECU ground reference will offset the measured signal.  You can usually observe this with an analog controller by for example turning on the fan or head lights and you will see the reported AFR change.  Some of the cheap ones you can even see the wideband heater turning on and off in the analog signal.  A further issue is most of them have a very poorly calibrated DAC - i.e the documentation may say for example it outputs 2.5V at 1.00 lambda, but if you test it you find it is actually only 2.3V. 

An Alternator Control function has been made and should be available in the next major release version.