Before Doctoring, should I clean out my USB drive?

[Audemars02]

Over the past month or so (going back to 1.3.1), my Pre has started to have some random Luna Restarts (about 3-5 per week). From July thru December, I maybe had a total of 2 restarts, but now I am getting more than that per week.

I have done a significant amount of patching and homebrewing--but nothing beyond using Preware or webOS Quick Install for both Patches/Tweaks and homebrew--and never used any Themes. Also, I always uninstall patches prior to all software upgrades.

So, here are my questions that I have yet to see any definitive answer to:

1. Any suggestions to my restart problem before I do a Doctor? I have used Jason's webOS Quick Repair utility in the past prior to a Doctor, but it doesn't appear to be 1.3.5.1 compliant yet. Is it worth waiting for Repair Utility to be active first?
2. Any reason to do a full or partial erase before Doctoring?
3. The last time I doctored was when webOS Doctor still erased the USB partition. Since it no longer does that, should I keep everything there intact, or should I delete the USB section first? My concern is that if my problems are due to some conflict on that partition, a doctor isn't going to necessarily fix it, and I just did all that for naught.
4. If I do decide to just delete anything from the USB partition, are there any folders (including the hidden folders) that I should not touch? I do not want to lose all my application data / games results / etc, and without a total understanding of the post-1.3.5 method of storing apps and data, I don't want to do anything to lose any precious data!
5. Any other suggestions?

Thanks for everyone's help.
Adam