Adamw

Unfortunately the adapter board on this ecu is quite old and doesnt have the knock input available on any user-accessible external pin.  If you wanted to return it to our UK office they could add a couple of wire links to make the knock input available.  

Probably not in a traditional log, but we have discussed having some of this type of info placed into a trigger scope capture before, this would be the only way to have enough sample rate for engine position.  Even at 1000Hz, a 1ms inj PW is only going to be a single data point, the typical rule of thumb is you want 10X the sample rate of the shortest event.  Most likely some of it would have to be assumed/calculated data rather than actual captured events too, as it would require a crap load of processing to get all the individual cyl trims and dwell times etc.  

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

Knock typically initiates well after TDC, 10-50ATDC.  On a well optimised engine the peak combustion press will be around 15ATDC, on poorly optimised knock limited road car engine the peak cyl press will be more like 25ATDC, when knock does occur the biggest shock wave is often the first one right around the normal PCP but it can sometimes start off smaller and grow during the expansion phase so this is why you want to monitor for sometime after this point also.
 
  

The sensors are wired in series with just a single wire going back to the dash.  As far as I know both sensors are the same, so measure 1 and double it.  

If your engine runs then the base map has done its job, you now need to tune it.  Typically to find the best switch points for a switched cam you do a run on the dyno with VTC off and another with VTC on full time, then overlay them, where the lines cross is your optimum switch point.  Im pretty sure the last VTC RB i done was on around 2000 & off at 5300 but it was quite a few years back and im going from memory.  Im not sure if I even used a load condition.

correct, a band pass filter centred at 8K.  

Also dont mistake active state with drive type.  Regardless of active state a PWM output will always be a low side drive - that is it can only supply significant current to ground.  It is pulled-up to 12V when not driven low but it will only be able to provide about 5mA in the high direction. 
I would expect that device you have if it is designed for PWM wouldnt require any significant current but who knows.  You can check by measuring voltage at the device when the aux is in a high state.   

Your idle postion starts at 9.1%, this comes from your base position (7.6%) + your start-up offset (1.5%), you can see the start-up offset is decayed away over a few seconds and at log time -1:36 the idle position is back down to base position.  But Your RPM is still at 1900 at its point - it is above your RPM lockout so idle control will never kick in.  
So your base position is too high for 40°C and possibly your start up offset is too high.   At -1:35 your AC turns on which adds another 0.8% offset and makes things worse but that is probably ok provided the other two were closer to correct.

 
Overrun fuel cut is active because your APS is below the APS threshold and RPM is above the de-activation RPM. 

I would use 8K for a EJ207.  Attached is a spectrograph from our EJ205.  Frequency is the Y axis, you can see at 7, 7.5 or 15K there is not a clear difference between knocking and not knocking, at 8-9K it is much easier to see.  8K works good in our car.  

8k narrow should work nicely with that.

I would use 8K for a EJ207.  Attached is a spectrograph from our EJ205.  Frequency is the Y axis, you can see at 7, 7.5 or 15K there is not a clear difference between knocking and not knocking, at 8-9K it is much easier to see.  8K works good in our car.  

Please post a copy of your tune and your log file.  There are a lot of parameters that can affect this behavior and you're not providing enough information to make any specific recommendations.

I would say you have just kissed the RPM limit.  You just dont see all the detail due to the logging rate.  In the next firmware the limit capture for logging has been improved so that the status and limit flag word will stay active for a minimum time so it is always captured even in a slow log.   

You havent really provided any info to help.  The loom manufacturer should probably be the first port of call for questions about which ecu is controlling what functions and what needs to be set up in the engine ecu to making the trans ecu happy, all this would have had to be planned before making the harness. 
If you cant get that info from the loom manufacturer then if you can provide all the loom documentation and a copy of the tune and log from the ecu and a better description of the problem you are trying to solve then we may be able to offer more relevant advice.   

If it is an EJ20 based engine I would try normalised mode, then variables like RPM, load, distance from the sensor, mechanical noise etc has very little effect on the threshold.  Copy all the settings out of our WRX11 base map.

Correct, either splice the two 16AWG output wires close to the PDM to a single larger wire, or run the 2 wires all the way to the device.  Splicing to a single wire close to the source is typically considered the preferred option for high current devices as with the shared wire option you have more risk of overheating a wire if there is some factor that causes the load to not be shared equally between the wires such as a bad crimp or broken copper strand etc.

Yes, this is the oscillation that I mentioned above.  The PID needs tuning.  I would start by dropping the max min DC down to 90% as shown in the EvoX throttle settings in the help file and you will possibly have to reduce proportional a little too.  

Yes this appears to be a PID tuning issue.  I cant really make any suggestions for PID values as I have no personal experience with the EvoX throttle so you will need to experiment yourself.  Based on other cars with similar throttles, my guess is most likely derivative gain needs to be increased a lot.   
To tune e-throttle PID I typically set up a time plot with TP main and E-throttle target on the same graph, set up the E-throttle target table so that it quickly steps between 20% and 80% with a small pedal movement.  With the time plot running live (engine off) move the pedal and watch how well TP follows target, how much oscillation, overshoot, undershoot etc.  Change only one P, I or D gain at a time and test each change.  
Target set up:

It doesn’t say anything about degrees or degrees absolute retard mode.  It is saying not to use a fuel cut with aux injection which is what I already stated above.

Yes this appears to be a PID tuning issue.  I cant really make any suggestions for PID values as I have no personal experience with the EvoX throttle so you will need to experiment yourself.  Based on other cars with similar throttles, my guess is most likely derivative gain needs to be increased a lot.   
To tune e-throttle PID I typically set up a time plot with TP main and E-throttle target on the same graph, set up the E-throttle target table so that it quickly steps between 20% and 80% with a small pedal movement.  With the time plot running live (engine off) move the pedal and watch how well TP follows target, how much oscillation, overshoot, undershoot etc.  Change only one P, I or D gain at a time and test each change.  
Target set up:

The S13 and S15 plug-in ECU's have a 7Bar MAP sensor onboard, you just need to run a vac hose to the ecu.  It will run and drive gently with minimal adjustments to the base map, but it will need tuning before any significant driving.

yes.  I always like to do this to get it more accurate though:
Initially set to calculated ratio. Set staged injection table to 0 (all fuel through primary). On the dyno hold the engine at a medium RPM, medium load so you are up around 50% DC on the primary injectors (say 3000RPM & 30%TP for example), adjust fuel table so that the measured lambda is close to target lambda. While still holding at same RPM/Load, change staging table to 100% (all fuel now through secondary), you will get a little lean blip as it swaps over but if the ratio is correct your measured lambda should settle on the same value it was at before.   If lambda did change significantly then adjust Sec/Pri ratio and switch back and forwards between 0 & 100% staging until lambda is the same regardless of which injectors are being used.   

Assuming you can get ABS hubs/sensors for the S13 then they can be used, and the falcon ones will work also.  

You either have a bad connection or a dead sensor.  But since the problem apparently occurred after you disturbed the wiring I would lean more towards a bad connection.  Set up a multimeter measuring the resistance between ground and trig 1 pin at the ecu while wiggling/bending/yanking/pulling all the relevant bits of loom to find the issue.  You will see the resistance jump around when you find the problem spot.