I guess you'll find that out when you count out how many turns of the bolts it takes to fix the problem you've already got. Really, a different number of turns on the limb bolts is meaningless. The key is to adjust the weight of both limbs to where they match. Right now, you've got one limb (bottom, most likely) stronger than the other and that's why the bow paper tunes with the nock low.

Axle to axle length is measured center to center of the axles. That's correct. Brace height is a little touchy. Some outfits measure to the center of the rest mounting hole, some to the throat of the grip, some to the belly edge of the sight window. I don't know how Bowtech measures it. Maybe one of the Bowtech tycoons can help you out there or check your owners' manual.

Bowtech measures to the grip throat.

I had a problem with the trap door and fletching clearance also. It just wouldn't drop out of the way fast enough even on the lightest setting. I ended up putting on a drop zone and voila! end of problem.

This is a somewhat common complaint I hear w/ the MBG. I personally have not had that problem with mine, but I have seen it on other folks' equipment.

I would suggest setting everything back to "even", and trying a different rest and see what happens.