I am guilty of reading into...rather than simply reading your initial post. SmallTownGirl13 has clearly done a better job than I of understanding what you want. I misunderstood your OP to mean that you WANTED to roll back to the earlier version and root. I apologize. I sometimes have a problem where I don't RTFQ (Read The Full Question) before interpreting what is being asked. You can (as STG stated) re-root your phone with the new exploit. Might I also suggest that you download
Doomlord's Voodoo OTA Rootkeeper from the Market and (hopefully) protect your root from losing it with future updates?
FYI:
Superuser is an app but it's not installed like other apps, and so it can be deleted, but with a root-based app explorer. Since it's in the root portion of the phone's storage, you have to be rooted to remove it.
Clearing data will not delete anything from the apps storage area. What you can do to be sure you're back to stock before going forward is to do a Factory Reset, however it will delete ALL your apps, ALL your personal settings, and essentially the phone will be the way it came out of the box. It's a drastic measure but sometimes its the only way to resolve nagging problems that just won't go away.