Ok, what I'm going to do is try and tell you the quick-n-dirty bare bones minimum direction towards getting your frankenpre 2 up and running, which may go against best practices, and won't be the advice I or most others would normally give, but it's your choice if it's what you need to do. As always though, if in doubt, follow the wiki.
I also heard once about someone claiming to use a Verizon doctor straight up to set up a frankenpre2. If there's one corner I wouldn't cut though, it would be making a proper Sprint/meta-doctor (It's SO not as hard as you might think, don't be intimidated by linux terminal...think of it just like the command prompt in windows XP). I've never tried to verify the straight up Verizon doctor claim myself, but I imagine that it would differ not only in the included apps, but network activation settings, maybe app catalog settings, and other under-the-hood things. Edit: See Post #9 for booyapre's personal observations after using the straight VZ doctor. I do suppose you COULD try the Verizon doctor straight up first, and if it doesn't work well, go back and do a proper sprint meta-doctoring. Note also that you CAN separately get both SprintTV and Sprint Nav onto a frankenpre2 later on if you use the proper sprint meta-doctor for the main setup (Info on these can be found in other threads).
2. Without getting into it, I'm going to tell you not to worry about these right now. They are not needed if you use the meta-doctor on the new phone. What I would suggest instead is reassemble your old Pre- when your done, using the spare comm board you removed from the Pre2, and hang onto that reassembled Pre- so that you can still boot it up in case you do need to retrieve those old tokens some day.
3. Again, let me try and keep this simple, even if it means I don't answer all your questions. No, you don't absolutely need to copy your Sprint PRL if you use the meta-doctor on the new phone. What you SHOULD do at least is update your PRL (and maybe your "network settings" too) from the preferences menu in the phone app of your Pre- before powering it down for the last time for taking it apart. That will program the latest PRL into the Sprint comm board itself before you transplant it into the Pre2 body. (Again, if you reassemble your old Pre- like I mentioned before, you can always hang onto it and be able to boot it up and get certain files another time if ever needed, and not worry about how to do it until then.)
4. Notes/Memos and Calendar events should be synced to your webOS Profile "in the cloud" online, so they should sync back to the new frankenPre2 automatically after you log in for the first time. No need to manually back them up.
5. Technically no, you do not absolutely need to back up the Pre-. The only usual things that aren't backed up online that people forget are pictures and videos. Those are easily available in USB mode by dragging/dropping with windows explorer to your computer, and then later back to the new phone.
6. Eh, I don't think you need to do this. Your contacts and such are already backed up, and everything should convert and sync up again after you meta-doctor and log in to the new phone. Your profile doesn't need to be showing the newer webOS version ahead of time.