Yep - sadly, I found no substitute for factory reset.
http://androidforums.com/support-troubleshooting-evo-4g/141369-how-fix-froyo.html
On the new kernel page, there's a warning that the Clockworkmod may not clear everything out, and to switch to Amon Ra.
I'm gonna run out and get right on that.
For now - I just do a factory reset/restore backup whenever I flash anything and it's better - sure seems to restore the snap and pep.
Note that you can restore your desktop in Titantium Backup (save Personalize->Scenes first), find DESKTOP - that's it. Also backup your system Mail app and it'll save you a load of re-entering. Then backup everything with a Titanium shield - you'll get to keep any wifi passwords or Bluetooth pairings you've probably made while knocking one back and enjoying your new rom.
Trick to restore the desktop after a reset - just change one thing, then save that a scene with a dummy name - presto, the DESKTOP entry is back and you can grab what you need if you must do that one by hand.
If you manage your batch and backup level carefully, you can always get back with one click.
Happy rooted froyo-ing. Note the Quadrant scores we're posting in the other thread.
XDA - Netarchy-toastmod 3.7.7 kernel with Amon Ra endorsement
There's also a Clockwork to Amon Ra conversion thread somewhere. I lost it.