what do you mean by:
I had a hell of a time trying to get the bolts off of the rim so that I could align the cog correctly, but I'm not sure that I've gotten it yet.
are you trying to respace your rear hub to get proper chainline?
if so, don't. you'll have to redish your wheel as well if you do this. and it'll throw off the flip side of your flip/flop hub too.
sounds like you might need a different BB. measure your chainline front and rear.
and yeah, rim tape is your friend.