Adamw

Yes updated pinouts will be in the next release of PCLink which I believe is not far away.

I wouldnt jump to that conclusion.  If you want to diagnose a fuel mixture problem then you will need a lambda connected.  Without that we are shooting in the dark.  It might be more obvious to you as you can hear and see the engine running, but a log without that feedback is not very helpful.
 
The S54 Ethrottle has 6 ITB's (return spring on each), the linkage is very non-linear at the initial opening and Engine vacuum seems to have a large effect on them (I suspect the butterfly shaft isnt centered so vacuum pulls them closed, maybe a safety feature?)  It takes a lot of grunt to get open when there is high manifold vacuum.  Our E-throttle hardware is a bit borderline for driving these and some guys have trouble even after removing some springs.
 
This is normally the amount of throttle that the closed loop system is trimming the "E-throttle 1 target" to maintain the idle RPM target.  In this log however it appears Idle speed control is not even working - the idle status shows "speed not selected", which usually means a speed lockout is set up but there is no speed source.  I dont know if he has changed the map after the log was taken or whether there is something odd going on.

Ignition drives only get assigned when loaded into an ecu.  Load your map, store, then power cycle. Drives will then be assigned correctly according to your ignition mode.

Your PID settings look good enough - your target vs actual tracking is pretty accurate.
The numbers in your TPS calibration dont line up with the max/min voltages seen by the ECU though, so its like at clsoed throttle its actually reading -10% for example.
The biggest problem is that the latest log now shows voltages for main and sub both moving over a full range of motion, no 70% stop on the sub signal like you have configured. Try changing the tps sub percentage to 100% and get another log please.
If you look at the TPS voltages rather than the percentages,it shows TPS main as 0.66v minimum and 3.12v maximum. These should normally be your closed and open numbers. Your config has closed and open numbers as 1.051 and 2.972. The 100% value looks to match the steady state open throttle voltage of 2.97v, but it spikes above 2.97v up to 3.12v for a little bit each time you snap the throttle open. I'd suggest leaving open voltage at 2.97 for now but changing the closed number to match minimum value. At the closed end the throttle it has to get to several percent open before it will register any movement off the closed position. Try changing the TPS main closed value to 0.66v 
TPS sub shows 2.21v min and 4.93 max. Again your open value of 4.966V looks close enough, but your closed value of 2.698 means the sub sensor also wont see any movement until a few percentage points of movement. Try changing the closed value to 2.21v.
I also noticed something strange in your log - the minimum values are usually 0.66v and 2.21v, but  at 27 sec, 39 sec and at 45 sec it attempts to return to 0% throttle, but the voltages sit above the closed voltages. I'm assuming this is just because once it drops below the expected minimum it will stop driving the throttle shut, so its probably just physically at 2-3% open. Theres a chance though that your tps does have issues and isnt registering the closed voltages consistently. You'll need to change the closed calibration numbers and re-run the log with all values present to check.
 

It is correct that in theory you shouldn’t have more than the two terminators at each end of the bus, but in real life most OEM buses will still run happily with the extra termination resistor, so try if first. Some of the CAN messages may match the 350z but that is unknown.

Correct, DI9 & 10 just need to be set to off to allow CAN through.

Based on your log try these settings
main closed voltage: 0.95
main open voltage: 4.41
sub closed voltage: 2.56
sub open voltage: 4.93
sub 100 percentage: 60%
 
[edit]if that dip in voltage at the start of the log is not just an anomaly, and represents actual 0% TPS, then you need to use the value below. Does it look like the at rest position of the throttle blade is completely shut or does it look 2-3% open, and only fully closed when pushed/driven shut? Once you get it pretty close, can you run the calibration wizard to fine tune it?
main closed voltage: 0.66
main open voltage: 4.41
sub closed voltage: 2.21
sub open voltage: 4.93
sub 100 percentage: 62.5%

Pretty much finished. First startup in car vid at the link below.
 
https://www.dropbox.com/s/p73ni3uusoj6t7m/car pc dash small.mp4?dl=0
 

Since a 12 injector ecu may never be a big enough mover to justify a new hardware platform, another option might be firmware/software based solution that allows 2 ecus to be linked together in a master/slave configuration.  2 x Storms linked together would be a relatively cost effective option for those that need 16cyl sequential?

Serial numbers below 10000 need a couple of components removed from the PCB.  If you PM me your serial number and ECU model I can probably give you instructions if you are capable of SMT soldering.

The cable you are missing has part number #CANPCB.  This is what it looks like: http://dealers.linkecu.com/CANPCB_2
You can search for a local dealer here: http://www.linkecu.com/dealer-network/  Most dealers would not have this part in stock but our UK warehouse has them in stock so it wont need to travel too far.
 

If the ST185 dwell table works better for you then by all means please use it.  
 

Here is where you adjust that:

The logging will still be limited to the 100Hz or 40Hz limit regardless of the data source.
Although the ECU can still receive, process and use the data much faster if it is used for internal calculations - it will only be time stamped and written to the logging memory chip 100 times per sec.   
The maximum rate for transmitting CAN messages out of the ecu (for say an external logger) is limited to 200Hz.
 
 

Your triggerscopes look like they would work ok with your current settings but I would probably make a small change to the trigger 2 arming threshold table just to give us a little more margin of error.
Try it like this:

 
I suggest for the next little while that you carry your laptop around with you, then if it ever doesnt start again you can connect laptop and do a quick triggerscope which may show us what the problem is.

Hi Johnny,
You might need to explain better what you need help with?
If you just dont know where to start for the layout etc then maybe this video will help:  https://1drv.ms/v/s!AiYbYlZQuRHPkBKWqkFTOw1fcUZm 
So you know what Im doing, Red circle = Right mouse click, Blue circle = Left mouse click.

According to that factory wiring, all the shielding on the crank/cam signal lines connects to the throttle body ground. As per AdamW above you should only connect sheilding to a single source so it looks like you leave this alone as far as ECU connections go. You could disconnect just the sheilding wires from the TB ground and connect it to the ECU's shield ground if you want but make sure its one or the other, and dont disconnect the whole TB ground bolt as its what your ECU uses as its ground connection.
After looking at the diagram a couple of my comments above need changing:
On an AUTO engine the VTA connection is throttle position but on a manual, its just idle and "not idle" as you initially suspected so you will need to run without TPS or replace it with the sensor off an auto (or an aftermarket TPS)
The 12v/14v wiring shows you should use pin 3-7 (+B) as your input to the ECU as this wire runs from the output of the EFI relay. - do NOT use the BATT line as I first suggested. this appears to run directly from a permanent battery feed so I have no idea why it says "EFI relay"on the description. The other +B line on 3-1 isnt even shown in the diagram.
There are also 2x vacuum solenoids marked "VSV boost" and "VSV TB ICV", and something marked boost control. One of "vsv boost" or "boost control" will be your boost control solenoid, but the one marked "boost control - BC" looks to be high side driven from the factory (ie the ecu outputs +12v to trigger it). You probably want this connected to a PWM controlled digital output on the link but these are only available as low side drive (ie they ground the output when active), so you will need to rewire that boost control solenoid so the EFI relay or another relay feeds it 12v constantly, and the ECU grounds the other side to control it. Hopefully you can figure out what these do by looking at what they are physically connected to as I cant tell from the diagram which of the 2x boost related systems is the one you wire up as boost control in the link ecu, or what TB ICV does. You may need to connect one or both of these to get the engine to work correctly but I'm not familar enough with these cars to tell you from the wiring diagram alone.

I would say it is still mostly fuel related.  The 4 cells highlighted in blue below are where you are idling so you want to flatten those out a lot more.  It also appears you have very large injectors with no short pulsewidth data so this will make mixture quite inconsistent around idle.  If you cant get proper data for your injectors then I would suggest aiming for a richer target at idle and possibly reducing your fuel pressure a little.

I agree with Cam's comment that we are missing the ability to do traction disable by a virtual aux at present but you can still do want you want if you have a spare aux/ign/inj output available:
You set the aux to GP Output, set its conditions up so it goes true whenever your "AEM pot" is in the "0" position (most likely my example below would do it).  You connect this aux output wire to your "traction disable" DI so it will then disable TC whenever AEM knob is in position 0.  

 

from PLX's manual:

 
Note you dont need a cal table for a linear calibration, it will be easier for you to use cal 4, 5 or 6, like this:

Your problem is your cal table.  You have table units set to "Lambda", but you have entered the table values in AFR.  Enter your cal table data in Lambda units then if you want PC Link to display AFR, you change this in >options>units>options

Slightly off topic but perhaps relevant to the intentions of this thread.

I did some tests with a thermal camera, with the fuel pump running and the engine turned off. 

In this case, what heats up the fuel is/was when the fuel flows through the hot fuel rail bolted to the head, and then circulating down to the fuel tank and back through hot fuel rail again and so on.

Which is even worse when you have a surge tank to the fuel rail, which is probably why people think its the pumps making all of the heat.

If you slow down the speed of your fuel pump, and the fuel is flowing slower through the fuel rail then you're still transferring the same BTU of heat. (Half as much fuel flowing for twice the time through the hot rail)
If I leave the fuel pump running with a cold engine, it took something like half an hour to increase by 5 degrees. 
But with the motor running the fuel temperature increases almost immediately. 
Insulating the fuel rail from the heat of the head and I never had fuel temp issues again.



Fuel rail is dark blue item near the left hand side after insulating it with thermal paint, and putting plastic washers under the bolts that hold the fuel rail to the head.

EDIT: 

Found a pic of a close up of the fuel rail, you can see the hot bolts (now insulated) against the rest of the rail (darker colour)


 

Something like this will do it.  Note "0%" in the boost table ratio table means you are using boost table 1, "100%" means you are using all of table 2, 50% would be a blend halfway between table 1 & 2.

Ok, you still didnt tell me much about your setup and what you want to do but hopefully this example will give you some ideas...

 
So in this example I have set up a virtual aux to "switch on" when wheel speed is less than 10KMH.  I have assigned this virtual aux to an axis in a GP Limit table, this will give us a 6000RPM limit when the Virtual aux is on and a 10000RPM limit when the VA is off.
I have then set up 4D fuel and ignition tables that are activated by this same VA.  Whenever wheel speed is <10KMH, the 4D fuel will add 10% fuel and the 4D ign will retard ign 20degs.

Your trigger pattern looks like it matches our "Swift ZCS32" trigger mode, please give this a try.