This is what I recommend and I have been told it works:
Root.
Flash GBRooted.
Flash GBDeodexed.
Go into Clockwork, go to Backup and Restore
Hit advanced
Click the back up you want
Then hit restore data.
You get a fresh system install AND all your data back. And, since it was from the same system, you shouldn't get force closes or anything.
Like I said, I have been told this works, but I haven't personally used it so proceed with caution.