[Pierre]

I suggest you get the swap manual from Jim Leach on this board. It's definitely worth the expense in saved time and aggravation.
The plugs by the fuse box is waht connects your engine harness to the body harness. The top part go to the engine and DME. They come with the S52 harness.
The third plug in most cases is for the Utomatic transmission. Some manual transmission cars have 3 plugs also. My M3 donor 5-speed had 3 plugs. It is at this plug that you need to run a wire to your cluster to make you mpg gauge work. Again, the manual describes the details of that procedure.
I have yet to get the car running. I am at the final stages. (EWS DME alignment.) I deleted my tool box and placed the battery in the battery box bolted to the floor of the toolbox floor.
My suspension is somewhat of a hodge podge, but until I get the car running, I won't invest into any componenets. The front was transplanted from the M3, complete. Bilstein Sport, Schnitzer sway bars and springs. My rear is currently stock ti since the M3 rear does not transfer. I am focusing on getting the mechanicals working and the car running before I deal with suspension and brakes, and eventually, the cosmetics
The AC transfers over complete. ABS modules, brake hydraulics at the master cylinder are different. They don't transfer over.
I hope this helps.