If I do that, and rebuild my system from scratch, what's the easy way to get my apps back? (you can tell I don't swap Roms much) I have TiBu. Re-downloading TiBu is no biggie, but I want to make sure it will have the back-up data, and can restore individual apps until I get a clean system.
If you don't have Titanium automatically scheduled to backup apps already, within Titanium go to menu->batch->and tap "Run" next to "Backup all user apps". It should not take too long to finish.
Shut down the phone and hold VolUp to restart. Do a Nandroid backup, just in case (Backup/Restore menu, Nand backup), then go into the Wipe menu and Wipe data/factory reset. You can also Wipe Dalvik cache while you are there. Then restart the phone from the main menu.
The first start will take a while and go through the initial setup process. Reinstall Titanium Backup from the market when you are able (I'd pay for a pro key if you have not already - it will make the next step easier.) I'd avoid installing any market updates for the moment.
If you cannot install Titanium for the same reason, something is definitely screwy.
Start Titanium Backup and grant it superuser rights when prompted. After looking at the Titanium change log screen, from the main Titanium Backup screen, do menu->batch->and tap "Run" next to "Restore missing apps with data". I would avoid restoring any system apps at the moment (anything colored red or green.) Let this run and then see what happens when you go into the market again - see if you can install system apps.
If you do have the market updating and installing apps, then you can either go through all of the settings for your apps to get them reset the way that you like. or you can *try* restoring some of the system apps in Titanium. I'd avoid the ones colored red (though because you are restoring from the same custom ROM, they *should* be all set.) You may want to another Nandroid backup before trying to restore system apps in Titanium, though.
I just fired up my Eris after a long while and went to the market and was able to install a few apps, though Google Maps returned a "could not be found" error. It may be that Android 2.1 is just not being supported well by Google at the moment and you may want to *consider* moving up to the Gingerbread ROM GSB or Condemned if the market issues continue.
One quick note - you will lose call logs and SMS/MMS messages if you do this. Do you need these to be preserved?