DO ITTTTT!! To make everything easier, depending on the year, swap transmissions too. only problem i ran into putting a r90 motor in my 65 was the ignition. going from a wire harness for electronic ignition and trying to make it work for points was tough. this all again depends on the year of the motors though. exhaust was no problem though as i wasnt using stock bmw mufflers to begin with, if you're swapping, you'll need his mufflers to modify because your headers are smaller.
as for the final drive...leave it if youre putzing around town, it turns into a completely different animal. touring or commuting or if you just that concerned about mpg, change it. i left my stock 32/9 on and the first test drive after everything was squared away scared the @&!% outta me! no clutching or anything, just a handful of throttle and i stood my 65 up in the air almost falling off the back! now i don't wheelie on purpose but it wasnt the last time that happened. if i'm ever inclined to ride with gusto, 1st to second is a wheelie and 2nd to third is a wheelie...just saying.
the most valuable piece of advice i ever got was to WRAP YOUR FRAME! go get some blue painter's tape and make a good 4 or 5 layers on your frame lowers to protect the paint. that motor is small but awkward to take out even with someone helping and i promise that it will hit and/or be rested on the frame at one point or another. be careful not to hit the neutral switch and bend or damage the tabs.
also, it's common to remove or slide back the swingarm in order to pull the trans, then pull the engine. not unnecessary. it was easier for me to unhook the driveshaft, pull the rear motor mount, then tilt the motor and trans up towards the backbone of the frame, THEN pull the trans.
if i think of anything else i'll post or if you have questions, feel free to ask. i did the job on my own so it's not impossible or even drawn out, it just requires alot of patience. good luck.
SUPPORT HYBRIDS!!