I pulled a django project repository (git) to a FAT32 drive and made some changes but when I went to commit, every file is out of date because of it's mode (i.e. - was 100644 is 100755) that's because of FAT32 right? I haven't ever really thought about this, do I just need to work off of a different filesystem or is this not a big deal in the long run?
I think you want to tell Git to ignore the file permissions. See this question: How do I make Git ignore file mode (chmod) changes?