So now that you're got a winterizing additive in the tank, it starts fine? Sounds like gelled fuel... Good thing -- an easy fix!
Some details on what you are starting with for a gearbox might help with information: do you have an M46 now, or an automatic? Some of the tbricks info may not apply if it talks about how to swap from an AW70/71/L to an M90, since the ZF automatic in the diesel cars is a different setup than the gas AW trans. The ZF trans crossmember is the same as what an M46 uses. The trans and motor mounts are also matched to some degree, so switching from one type to another type on the trans and not changing the motor end might make things sit funny...