I had this same issue last year on my restoration, and I was a little stumped at first. I would consider removing the motor with the bike resting on the front wheel and center stand. I cant find a good way to raise the bike on the typical MC jack because of the lugs for the two kickstands get in the way.
There is minimal clearance to get the thing out. You can do it the hard way or the easy way. Since your doing a resto anyway, you may as well take the easy way. It just (seemingly) involves more taking apart. But you will end up doing most of it anyway.
- It is assumed you have disconnected all fuel, electric and mechanical linkage to the engine
- Remove real wheel, swing arm and disconnect the universal joint.
- Take off the front engine cover, and the top cover
- Remove all the transmission housing bolts. This will require removing the air box, I think.
- Remove the exhaust.
- If your not planning on repainting your frame now is the time to cover your frame around the engine with cardboard and tape. You will bang and scrape the frame on the way out and back in again.
- Support the engine and remove the engine bolts
- I think I took the trans out last and put it in first. Not sure. But it will be fairly obvious what will and will not work at that point.
Reinstalling the engine was easy. I had the frame resting on the ground and was then able to get the engine in the frame and then move the frame around to line up the bolts.
See my reassembly thread:
http://www.bmwr65.org/cgi-bin/yabb2/YaBB.pl?num=1346783584