Adamw

Ignition outputs are also lowside drive.  Also only pulled up to about 6V.

Yeah Im not convinced the cam movement would be the issue either.  In VVT engines you can move the cams around 40 or 60degs in some cases without much consequence.
As for the other comments about knock control, it is actually pretty rare to use knock control when tuning as it will often work against you - pulling timing out when you add timing and adding timing when you remove timing etc (a bit like trying to tune a fuel map with CLL enabled).  So it is normal to tune the ignition map with knock control off, then enable it and tune knock control only after you have a known knock free map.  
 

For a supra plug-in you will need the CANJST cable, https://dealers.linkecu.com/ADA_2.  It doesnt come with the mating female receptacle, you can buy that separately (https://dealers.linkecu.com/DTM4F), or you will probably find it locally pretty easily too.  

You need to contact the dealer that supplied the ecu for the unlock code.  

It is an XA series.

You generally want to make it richer as load increases since cylinder pressure is higher so there is more heat and the engine is more susceptible to knock.  More fuel reduces combustion temps and makes it a little safer.  
With a big road car engine like yours peak torque (hence peak cyl pressure) will occur at WOT around say 3-4000RPM so this is the area where it is most prone to knock and needs to be rich.  Some may choose to lean it off a bit at higher RPM past peak torque but generally just a flat value across all RPM's is a good starting point.  With most NA engines you will achieve best power at around 0.9 Lambda, so this is where the "12.7 AFR" came from.   
Note also the values in your table will only be relevant if your wide band controller is set up with a stoich ratio of 14.0.  Most common ones have a default calibration of 14.7 as stoich, so stoich will always be 14.7 regardless of fuel.  

Yes I would place the switch in the 12V supply.  The main ground is often connected to a common ground plane internally for grounding other devices such as sensors etc, so if you cut the main ground you can end up pulling high currents through a sensor that wasnt designed for it.  

Can you drop the Sec PW lockout down to 0.8

Assuming it is a naturally aspirated engine I would put 12.7:1 in all the red cells and 13.4 in the blue cells.  For the lower load cells at 4000-7000 I would just carry the same value right across that you have in the 3000 column.

Yes, that is what I was suggesting.  Perhaps my wording could have been better.

Static voltage would suggest the pinout is wrong.  I have seen some mitsi wiring diagrams that have the numbering reversed compared to what is molded on the connector so the first thing I would try is reverse the pinout - ie swap position 6 with position 1. 

Melted plug electrode is generally pre-ignition.  With detonation you will generally break things before you melt things, but in some cases if you have relatively strong internals (forged pistons etc) they will handle the mechanical impact of the detonation for long enough that it can generate enough heat in the combustion chamber to cause pre-ignition so the damage is done by the pre-ignition but the root cause is detonation.    
Pre-ignition is something causing the mixture to ignite before spark has occurred and can generate extreme heat since the combustion energy is not all going in to expansion.  Pre-ignition is most often caused with lean mixtures under high load, or when there is something "glowing" in the combustion chamber such as a wrong heat range spark plug, lack of coolant around the spark plug/chamber or something like a fire ring on the head gasket that is too small and hanging into the chamber.  On older engines it can be carbon deposits etc but since yours is fresh you can rule that one out.  Or as mentioned earlier heavy detonation can cause it also.
Was it running ethanol or petrol?  Were the injectors new?  What sort of power was it making before this happened?  The ignition timing in your map is pretty extreme for an evo - generally you are well down in the single digits by 20psi on petrol - was that a prove ignition table or something new?

It is a G1 "LEMV5".  Really need to see inside to see what type of triggerboard it has in it - these ecu's need a dedicated board to match the engine trigger, you cant change trigger settings via software.  Not suitable for an LS as it only has 3 ign outputs, so typically only used on distributor V8's.
It is PC tunable.  Personally I wouldnt bother fitting one as a new install today, far enough for an existing install, but hard to justify spending time and money installing something so dated and limited.

Yes, just put gear on 1 axis of your base DC table.  Or if you want more control variables you can switch between 3 different base tables, say have 1 for 1st & 2nd, change to table 2 for 3rd & 4th and table 3 for top gear.

one clutch pin needs to be connected to an ignition switched 12V source, the other to an aux.  

If Allow CAN antitheft is off and there is no antitheft DI assigned then the antitheft status will just show whatever was last left in that memory location so is not relevant.  "Engine Kill" will be active if there is anything ECU wise attempting to prevent start up. 

B5, B6 or B7 was the original cam and crank sensor grounds.  You can splice them all together or do them seperately, no advantage either way electrically.  BTW, the pinout in the G4X manual is a bit more complete than the G4+ one, so you may find that helpful.  Copy here:  http://linkecu.com/documentation/TS2JZX.pdf

Ok, sorry I wasnt paying as close attention as I should have been...
There is something wrong with the crank signal.  In your scope I have marked each falling edge with a small pink dash.  As you can see there are 35 falling edges per crank rev, there should only be 24. 
The 24X wheel is a weird two row wheel and the matching sensor actually has two sensors inside and one subtracts "teeth" from the other.  So it seems either that crank sensor is failed or the wrong one so some of the teeth arent getting "subtracted"..  

No, all the ecu needs is an edge that rises above 1.5V and falls below 1.0V, which looks good in your scope.  
Since I dont see any obvious reason why the multitooth option isnt happy, can you try this:
Change trigger mode to Subaru V1-6, store and power cycle.  The rerason for this is changing to a completely different mode like this causes a re-initialisation of all trigger code and settings. 
Then change back to Multitooth mode, 24T, cam pulse 1X sync mode, falling on both trig 1 & 2.  Store & power cycle again.  Then try cranking, If still no good like that can you do us a short log of it cranking and another trigger scope.   

Try this one.  
amendedmap7.7.2022.pclr

You can wire them in.  I would probably just leave the IAT off if it is drivable now.  

You dont need to connect a boost gauge since the ECU already knows that.  
There are 4 spare AN Volts on one Expansion plug, so 3 of these could be used for the wideband, oil temp and press.  
The Ethanol sensor will work better connected to a DI and the IAT will be easiest with an AN Temp input.  The DI's and AN Temp are on the 2nd expansion connector so you will need another XSL for those.  

JST XA series

Looks usable now.  May still need further PID tuning, but it is in the ballpark.