1. What safeguards are part of the BMS methanol kit and JB4?
2. What happens if the pump stops spraying or you run out of methanol while running map 3?
the Fail safe will revert the map to 0, I have run out before.
3. Is there some indication that you are out (sound, dash light, etc)?
yeah, the car has no power 
4a. If you install the methanol kit and don't want to use it 100% of the time can you just load a different map (map 2 or map 5 for example).
only runs on map 3 (progressive meth mapping)
4b. The methanol injection is actually controlled by the JB4 correct?
yes and the fsb, which gets power from jb4
4c. As in, it isn't spraying unless the JB4 tells it to?
yes
5. Also, is it better (with the stock turbo and FBO) to run dual CM5, CM7, or CM10 nozzles?
two cm5 nozzles would be better you can run one cm10 or two cm5 possibly cm7 and cm5 for dd depending on use and when you activate (psi)
6. Also, does anyone know of a beginners guide to logging with the JB4? It's my understanding that you should definitely do logging if you are going to be using methanol and/or higher level maps on the JB4 but I cannot find a lot of well organized information on how to interpret this or how to start.
if you use the bluetooth, you can log automatically and post on n54 or send to burger for review.
7. Finally, does anyone know if the bluetooth interface for the JB4 is compatible with the newest version of the JB4 for the m235i (the version with the OBDII CANBUS interface?) It seems like it would make logging a lot easier.
Yes it does, I use it. Yes much easier