1) will the longer drive shaft bolts with the lock washers work well / better?
You really should get the right bolts, that is the shorter ones. BMW went away from the long bolts that used split lock washers. The washer would break, thus releasing the tension on the bolts. Short bolts, clean and dry, with blue loctite is the way to go.

2) what kind of torque does everything need when putting it back together? My guess based on what was on there is 50lbs on the flywheel bolts, 25lbs on the clutch bolts, and closer to 100lbs on the swing arm bolts. The drive shaft seems like you just tighten them as much as you can with a short wrench.
What does your manual say? Snowbum has torques listed on his website.