The easiest way to wire it up is to get the stock wiring harness. I see that it is a swap into a 91 GTI. If the swap came from an OBD1 MK3 VR6, then I would get the complete wiring harness from the engine to the fusebox just like you would use for dong the swap with the stock ecu. Once you have the stock wiring installed you can just simply tap into the stock 68 pin ecu connector, or cut the ecu connector and run the wires into the car and wire them to megasquirt. The first option would be the best because your would be able to switch back and fourth between the megasquirt and the stock ecu. Paul has a good writeup on both the dizzy vr6, and the coilpack vr6 here:
Dizzy writeup:
http://forums.vwvortex.com/zerothread?id=3359198Coilpack writeup:
http://forums.vwvortex.com/zerothread?id=4261092For the dizzy vr6, you will need one BIP373 coil driver, or you can use a 1k ohm pullup resistor from D14and use the stock coil and coil module. For a coilpack vr6, you will need either 3 BIP373 coil drivers, or you can use 3 1k ohm pullup resistors off of D14 to run the stock coilpack via the stock ignition module. Pictures of both are below:
Pull up resistor circuit: (Use a 1k ohm resistor where the picture shows a 750)
similar to this circuit in the ms-extra manual:
http://www.msextra.com/doc/ms1extra/MS_Extra_Ignition_Hardware_Manual.htm#bosch
BIP373 Wiring:
http://www.msextra.com/doc/ms1extra/MS_Extra_Ignition_Hardware_Manual.htm#mulitcoil
I would also do the idle valve when you install everything else so you wont have to go back and do it later. The instructions for installing a bosch PWM idle valve are here:
http://www.msextra.com/doc/ms1extra/MS_Extra_Hardware_Manual.htm#Fidle