Changing the emails is possible by editing a particular file, possibly qa-util-emailer.php. I can't find documentation about it on this site but it's briefly mentioned at the bottom of this page.
I'm not sure what your last bullet point is doing but you can change a lot within custom themes using $this->request. If not that maybe a widget plugin?
For everything else, what I do is add special comments at every place I make a change that includes my initials, for example:
/** SV: notifications off by default */
Then when I upgrade, I rename the old Q2A installation folder and copy the new one into its place, so I start with a blank canvas. Then find all the bits of code I modified in the old codebase and copy the changes across to the new one. On Linux I use this command to find what needs changing:
grep -R "/\*\* SV:" .
On Windows you can use Notepad++ or another method. It may be a little time-consuming if you made a lot of changes but it works well for me.