There are about 4-5 file edits needed for CMPS. Assuming that you don't use a program like Araxis merge to do your upgrade then your upgrade steps would (a) upgrade to 3.0.7, (b) re-install any hacks including the CMPS file changes, (c) re-install any master templates [in the case of CMPS it'd be just running the installer and choosing the template only option].
The settings for your custom pages are stored in the tables that were created when you originally installed the CMPS. As long as you don't wipe out your tables or choose "Uninstall" from the CMPS installer then those tables will remain out there even if you completely wipe out the file modifications you did and install a fresh copy of 3.0.7 -- you just need to redo the file changes so that it can see those tables again.
Now your other hacks on the other hand..... you'll have to make sure that they even work with 3.0.7 first.