How can I remove traces of my phone ever being rooted?
As far as I know, doing a factory restore on the device should eliminate anything left over the device.

Usually the process goes:


Revert back to  your earliest NANDROID backup (that you should have taken right after you rooted).  If you don't have it, then flash a stock ROM.
Run the unroot reversal process (in this case you ran an official update)
Remove any left over root applications (SuperUser app, etc.).
If necessary, wipe the device by restoring to factory settings.


If I'm missing anything, leave a comment and I'll update this.