I think this problem would've been a lot easier had I not decided to make the actual brainfuck coding easier by writing a debugger for the Mac, which involved remembering how to code in Objective C, learning Apple's CoreData API that I'd never used before (which was entirely unnecessary for this task but it should make my next Mac application easier to write), and then ended up writing the last 1/4 of my brainfuck code on a windows machine using emacs, so my debugger did me absolutely no good.
I scored 6945, although I'm absolutely certain that if the deadline wasn't today I could've significantly cut that down by the simplest of optimization. --Wooble