Which RUU did you try running? It would have to be the Ice Cream Sandwich RUU because you will not be able to go backward in software with s-on. Also, since you are s-on, the bootloader does have to be relocked to run the RUU. I don't know why super user would cause a boot loop... I have not heard of this before.
Check your bootloader and make sure it is ****RELOCKED****
If not get into fastboot with adb reboot bootloader then run command fastboot oem lock
Download this RUU: Shipped ROMs
Get the phone into fastboot usb mode either by connecting to the pc and using adb reboot bootloader or manually get into your bootloader by doing a battery pull and then holding volume down+power. Then select fastboot. When plugged into the pc you should see FASTBOOT USB
When in fastboot usb, run that RUU and follow the instructions it includes like disabling HTC sync, screen saver, etc...
If you want to try getting rooted again after the RUU, you can unlock the bootloader again with the same unlock token you already have.
You will need a custom recovery, I would suggest 4ext recovery, especially being s-on. Flash that through fastboot after unlocking with fastboot flash recovery 4ext_recovery.img
Then I would download a fresh copy of SuperSU.
Get that here: http://forum.xda-developers.com/showthread.php?t=1538053
and download the one named CWM-SuperSU-v0.99.zip
Flash Super su through recovery and you should be rooted on the stock rom! Good luck!
Will running the stock RUU UNROOT my phone? If so, I don't remember the token or the method I used to root it in the first place. Can you please clarify what token to re-root you are referring to and how. I am really looking to S-OFF to but a little concerned being a noob at this stuff. Thanks guys