Upon rooting, I think you pretty much need to bite the bullet and expect to spend some time setting things back up. Once you're rooted, you can use Titanium backup to restore everything in the FUTURE, but first round there'll be some rework.
Get an account on AppBrain and sync; that'll make it easy to reinstall all your apps.
Some apps sync against a website and your data will be downloaded once you reinstall and log on. 3banana does that with snaptics.com, Astrid tasks can be set up to do that with rememberthemilk.com Cardiotrainer links to a companion website.
Some apps save settings and data to your SD card, and will come right back the way they were when you reinstall. Tapatalk, Aldiko and SecForms work that way.
Some apps don't do it automatically, but will have a backup/restore menu option to let you write setting out to your SD card - for instance Doggcatcher does that.
I think a lot of your Sense settings (home screen setups, wall paper choice, etc) are toast. You'll just need to redo until you can use Titanium.
Bottom line: you won't loose everything by any stretch of the imagination, but you'll spend some time getting things back the way you like them.