I'm really intrigued by what all you're doing that you have this kind of problem. I maintain a pretty complex vimrc, and deploying it is normally just a git clone. I've never had any of these issues, and when I started at google (which provides a nice collection of internal vim configs and plugins), combining the two and getting everything set up took me O(hours), not O(days). What are you doing?
I simply updated mvim and :E stopped working on OSX.
I could work around with NERDtree, but its one of those things turned into a timesink when I didn't need it.