Sucks sam! But hey you were gonna do a swap anyway right?
As for the swap to clear things out, I would highly suggest against trying to "shim" the motor to use the stock booster. And even if you do clear it you'll be F'ed on the other side because of minimal space to mount up the downpipes
Sam, use the E28 535i "hexgonal lookin" motor mounts for both sides.
No need to switch the engine mounting arms, unless you have a motor that was originally from a E34 then you need the E36 mounting arms.
I've used the G240 with the m50 and you will need to use the euro 323i Throwout bearing(cross-refernce it) and the back end of the m20 singlemass flywheel must be ground down to prevent it from hitting the oil pan. You could remove some material from the oil pan but its a good enough reason to get the flywheel lightened. Match the clutch set and starter to w/e flywheel you are using.
If you wanna be extra cheap, the m42 flywheel/clutch set/starter can be used too, not sure how long it'll last though.
Now get on r3v and do some reasearchin' there. Grrrrrr.