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.
Wait, that doesn't sound like a problem with your vim config, it just sounds like you had a broken version of macvim.
Have you considered that your usage is at fault as opposed to vim? Out of 127 plugins installed and even more tried I cannot recall ever having an issue other than having bound a key that the new plugin would have bound.
I know, I'm "holding it wrong". I don't care who's "fault" it is, I just don't have the energy to try and figure it out.
I guess I must be doing something terribly wrong, because I can't relate to that at all.
Perhaps some kind of package manager that auto-updates plugins?
My packages are static and I only update when there's a good reason to do so.