So I decided to make a thread to document most of the process. Last weekend I spent most of Saturday pulling the motor out of an 03 M3 with 48k kms. The plan is to run stock DME to retain OEM functionality and reliability (basically identical to Mike's car). I finally got the engine mounted on a stand and started removing some of the accessories. Here are a few pictures of the progress so far.
I bolted up the headers and they are definitely going to need the longer M50 studs. (S54 uses 35mm while M50 uses 42mm)
Then I got around to pulling the valve cover mainly to inspect the vanos bolts/gear. The bolts were still tight and the gear didnt show any signs of cracking. Its also pretty clean in there with no scoring on the cams or anything.
This is probably all I'll do for the next week or so because of finals coming up. Next I'll be dropping the oil pan and checking out the oil pump nut and maybe give it a tack weld. I know the oil pump nut is mainly a problem in the M52/S52 engines but I've seen guys tack the S54 nut as well. It probably wouldn't hurt to do it especially since I'll have such easy access.
I'll try and update this thread as much as I can. Hopefully it livens up the E36 section too since we need all the help we can get haha. Also, huge thanks to Mike for his help and knowledge!