MS2 does not utilize all of the stims circuits. The stim goes way back from before James and Dax brought us the Extra code.
Backwards LEDs generally survive, so do transistors I taught myself.
Do not go for AE until you are running, that LED again goes back to the early versions, not MS2.

As far as low imp injectors, they generally free flow about 4 amps each, put 3 together and that is still below the protection limit. If they get stuck on things will get hot but should not let the smoke out.

For the maps, calculate what your boost will be in KPA. Say in the 140 to 200 KPA range for the max pressure. Once you are tuning the MS will tell you.
But lets say 160 KPA will cover your peak boost, start at the top where they have 100 and overwrite with 160. Then interpolate the numbers below that down to max vacuum, say 20 or 30 KPA. The engine will idle in the 50 to 70 range and pull lower numbers in trailing throttle. Again once you are running the engine will tell you, you can not tell it.
With the RPM numbers, have a number below idle, say 500, this gets set a bit rich and is a catch to help save from a stall. Then a number at idle, say 800 and another a bit above, say 1200 to help transition. Two thirds of the way up you want a number that represents torque peak. This number may change once the engine tells you where the peak really is. This will be relatively important since all points below torque peak will be adding fuel but after peak up to rev limit an engine takes less fuel.
You do not need an rpm value after the rev limit, MS will refer to the closest cell, it does not need a look to cell as with some systems.

Timing will be similar, Your high boost timing should be in the 13 to 16 deg range. Your economy cruise will be 45 to 50 deg at the very low KPA numbers. Idle 15 to 22 or so. Do not let a drag race horse power junkie tell you the on power timing can be in the 20s unless you like changing bearings and piston rings. Do not go for the last few horsepower when you tune this, they do not matter for what you are doing.

Pistons, I would set the compression around 9:1, if you go for 8:1 you will have a gas guzzler. This combustion chamber is fairly resistant to detonation and you are better off with more pressure and less spark lead/ timing. The only thing I would want are piston squirters from the turbo block. They would require drilling into the main webs for their install. If you are not towing a trailer and on boost for 4 hours at a time then they may not be needed.