The last two questions I think I have are where do I obtain a recovery image if I use this root app? and after I root, flash in the ROM, and then flash the theme I want, are there any known issues or special operations I would need to know about or will the phone run as it normally would?
http://www.droidforums.net/forum/hacking-faqs/39254-sbf-root-unroot.html This will put your phone back to bone-stock 2.0.1 (You can find a 2.1 SBF image to flash onto your phone
if you look hard enough.) if you feel the need to flash back.
If you're referring to an alternate recovery image like SPRecovery or ClockworkMOD Recovery, you can either use RSDLite to push SPRecovery (best method but requires a Windows-based computer and an application off the net, USB cable, and the willingness to do it) or ROM Manager from the market, which
should allow you to flash ClockworkMOD Recovery and SPRecovery in from within the app. ROM Manager is not playing well with FroYo at the moment, however, so it's not a sure thing on the first try.
No special operations are needed to get your phone running again after you install a ROM, but all ROMs are constantly being tinkered with and updated, so known issues come and go. However, ROMs like CyanogenMOD are stress-tested to make sure as few bugs go out as possible, and the DroidMod team are working on a super ROM that should be out some time before the Apocalypse.