There was never an M5R1 4x4 with 2.9l bell housing, just 4.0l bell housing but the same pattern, lol
The current transfer case will bolt up to the 4x4 M5R1, and the 4WD controls will work same as before
You should use a 4.0l flywheel and clutch on the 2.9l engine with M5R1
You will need the clutch/brake pedal assembly from/for 1990
And clutch master and slave kit
If you have a column shifter you may what to get manual trans column, but optional
The Computer won't like the fact that the A4LD is now unplugged so will turn on the CEL(check engine light) but thats all it will do, engine should run same as before
You can source a 1990 2.9l manual trans computer at your leisure or not at all
The A4LD has a 4 or 5 wire NSS(neutral safety switch), just above the shifter arm, 2 of the wires are for reverse(backup) lights, they will need to be connected to the M5R1's reverse light switch
Usually Purple/orange(12v, key on) wire and a Black/pink wire(out to lights)
There is no "order" on the switch, its just an open or closed switch, lights off or lights on
The 2 or 3 other wires can just be twisted together, they are for the starter motor activation
Usually Pink and Red/blue wires
You can install a clutch switch, to re-instate the No Start unless "in neutral"(clutch pedal down is "neutral" in a manual trans vehicle)
The wiring and connector is there for the clutch switch, just has a "jumper" connector in place, pull it out and plug in connector to clutch switch
Leave wires by transmission twisted together