If you are upgrading you will loose all your file edits, and you can't be sure that all your hacks exist for 3.0.7.
To start clean, it is the best to use ImpEx, since it will import all standard vB data, dropping all hack information. Be sure to read the stickied notes in the Import System forum at vb.com before you start, and do some test runs.
If your hacks didn't modify standard vb columns, the upgrade should be functioning normal, but again i suggest you test.
vBulletin.com is still teh place where you can get an official answer to these questions.
What do you mean by "file edits", just the added code in the actual php files? Yeah I don't care about saving any of that. I just want it to work like a fresh 3.0.7 but with my members and their forum posts intact running on the new version. So Impex is smart enough to not screw up as long as it was only the php code that was changed? What about queries that changed mysql info? I am positive that I have ran queries before for VB hacks.