Adamw

Our ECU is not even connected to the ODB2 port so logging from there wont affect the ecu in any way.  

You can just put zeros in your 3D trim limit tables where you dont want CLL to operate.  
Not possible as the LTFT table uses a GP table which has a max cell count of 16 x 11, whereas the main fuel table cell count is 22 x 20.  If your Fuel table is 16 x 11 or less then you can use the import/export tool to copy it to the LTFT to get the same axes.

Sorry I missed this post.  Yes that will be fine.  
Since your "junction" of dissimilar metals in this case is on the amplifier board which has a temp sensor on it, any dissimilar metal junctions at or near the board can be compensated for with what is known as "cold junction compensation".  The main thing you need to be careful of is a connection in the thermocouple wires somewhere away from the cold junction compensation temp sensor - for example if the amplifier was in the cabin but you had a connection in the cable somewhere in the engine bay, in this case you have a junction that is at an unknown temperature so would need to be made from the correct metals. 

Ah yes, now I look closer some of it is caused by closed loop lambda.  Its pulling lots of fuel out in cruise conditions then when you come to idle it cant remove that trim quick enough.
I would change the CLL RPM low lockout to about 1600RPM so it is disabled at idle and when coming into idle.  The min Eff PW that I mentioned above will probably help a lot too.  

Yes, negative values in the 4D table.  "-5" in the table would remove 5% fuel.  

Deadtimes and SPWA below for those injectors on petrol at 300Kpa with a G4X driver.  Flowrate for petrol is 892cc @ 300kpa.  They will flow quite a bit less on E85 but I haven't personally tested them with it yet.  Your high VE will most likely be because the flow rate is too high for E85.  Similar injectors that I have tested flow 10-15% less on pure ethanol Vs Petrol.  
IAT trim needs to be disabled, set up the charge temp table similar to the example in the help file, which is usually a reasonable starting point for common single throttle plenum type manifolds.  
 

The second black plug (CAN PCB) is most likely plugged into one of the CAN ports.  You can connect the CAN wires from the CAN lambda using this, you can either get the mating CANF plug, or cut the black plug off and use your own connector.  
 
You can use the factory wiring but the plug will need to be changed.  The MAP sensor comes with the mating plug.  
 
It has probably been mapped in traditional fuel equation which doesnt use the injector size.  Just adjust the master fuel value until it runs with the airfuel ratio in the correct ballpark.  In the staged injection settings, set the sec/pri flow ratio to 2.2 as a starting point.  

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.  

You cant enable it with the engine running as it is a synchronous process that needs to be accurately scheduled with crankshaft position.  You need to enable it with the engine off, once enabled then you can change any setting you like, just the initialisation needs to be done with the engine off. 

So is the streering motor only connected via CAN, there is nothing connected to an aux output?

You will need one of these, it can be wired to the same bus as your lambda:  https://www.seeedstudio.com/USB-CAN-Analyzer-p-2888.html
Here's an old setup instruction video I done for someone else:  
 

Outside of idle conditions the throttle will go to whatever is in your E-throttle target table + idle base pos + dashpot offset.  If it went to zero during decel as soon as the RPM got low enough for idle control to engage there would be no air in the plenum and throttle is closed so the engine would stall as soon as you press the clutch in. 
You would normally have 0 right across the top row in your E-throttle target table, I noticed you have 3% above 2000rpm so that will hold it open even more.  

I've only had a chance for a very quick look, but some first observations:
Battery voltage is all over the show, sometimes 11.9V at idle, other times 13.6 at idle, sometimes 13.6V at high rpm, other times 12.2V at high rpm. MAP only reaches 66Kpa at WOT, I highly doubt that is correct.  If so the would mean the air mass calculation is wrong and differential fuel press calculation is wrong. In the ecu logs there seems to be some correlation with IAT, when IAT is high it goes lean, not so noticeable in the PC log. VVT is slow to reach target in some places in the PC log, not recorded in the ecu logs.   Your map is password protected and there are not many channels recorded in the ecu logs so not much more can be gathered from what we have here.  You really need anything that can affect VE and all the major parts of the fuel calculation.  VVT, Inj PW, charge temp, fuel press, Accel fuel, etc

There is a "user lockout" setting for LTFT coming in the next release, so you could use a GP output to set whatever conditions you like for disabling it.  This lockout will disable both the learning functionality and the trim.

Attach your ecu and dash config, i will set it up.

So do you want 0 output between 49.1-50.9%?  or only 0 output between 49.9 & 50.1%?

If I understand correctly I think you are asking for different LED colors depending on 2 parameters, you could use a mathblock to generate different values for various combinations of the DI and button.  There is probably a smarter way but something like below would generate 0 when both DI & KP function are off, 1 when Button function is on and DI is off, 2 when Button is off but DI is on, 3 when both are on.

 
You should be able to allocate nearly anything, can you give a bit more info.
 
Can you explain in a bit more detail what you want here?  Do you want to disable the whole keypad 1, or only turn off the button on KP1?  The Set/Reset controls at the bottom would do this.  

The JDM Evo9 has a factory clutch switch connected to DI8, Im not sure if the USDM model does or not.  Set it up to see if you get any status change on DI8 when pushing the clutch.  
Ideally you want the switch to change state as close to the top of the travel as you can  - without it being so close that you can accidentally trip it by resting your foot etc.  

A G5 plug-in board is in development but its main intent, at least initially, will be for any future GDI plug-in applications.  All the existing plug-in ECU's will remain as G4X for the foreseeable future.  G4X and G5 use very similar firmware so G4X will continue to be developed and G4X will continue to get most new software functionality that the G5 gets, with the exception of GDI stuff and possibly a couple of others related to hardware such as GPS. 

I dont think there is a firm release date yet and I have no idea where price will be.  PC Link will be basically the same as G4X and G4X maps should load straight in.

Ok this should be a decent starting point.  I currently have the RPM target calculation set to gear ratio only so the speed sensor doesnt matter.  Having speed in the calculation is more important for downshifts under heavy braking so prob not important in this case since you have no blip capability you probably arent going to be doing clutchless downshifts.   I have set maximum down shift RPM to 500RPM so the ecu will only control upshifts.  I have set up ecu logging to log the important bits at high speed for gear shift tuning.  Do some half power shifts to make sure it all feels like it is working before committing to any full-power shifts.  Attach a copy of the ecu log after you have done some test shifts.  
current 811hp map V1.pclx

Have you measured directly at the ecu header rather than at the coil plug?

So what voltage do you have on Ign 1 pin with ignition on, engine off?

Have you only got a wire connected to A21 or A22, not both?  
How are you checking the signal?

Yeah you will only need 1 fuel and ignition map for just variable boost.