About HTC Sync: The only reason you need HTC Sync installed is for the USB drivers that come with it. But the program itself has been known to cause conflicts. Make sure that HTC Sync is not running in the background by opening Task Manager in Windows and killing it if you find it lurking in there.
Here we go:
1. Download the correct RUU (ROM Update Utility) for your device from androidfiles.org. Make sure you download a Primo_C RUU for a CDMA device (no sim card) or a Primo_U RUU for a GSM device (uses a sim card)!! Also make sure you get the correct RUU for your carrier.
2. Charge the battery above 50% or for at least one hour. If the battery dies during the flashing process, you could hard brick the phone!
3. Run the RUU until the wizard comes up. While the RUU wizard is open, find the temporary folder it created. (Open Explorer in Windows and type %temp% in the navigation bar.) There will be two folders with long encrypted names. In one of them you will find ROM.zip. Open it with 7zip and extract recovery.img or recovery_signed.img. Put it in the location were you've installed Android SDK tools. This is the stock HTC Recovery and it is needed to run the RUU.
4. Boot the phone into bootloader (power off, hold down volume and press power) and highlight FASTBOOT using the volume rocker and pressing power. Then connect the USB cable. You should see FASTBOOT USB.
5. Open a command prompt in Windows and navigate to the folder where you installed Android SDK tools. Flash the stock recovery extracted in step 3 above using the following command:
fastboot flash recovery recovery.img
fastboot flash recovery recovery_signed.img
fastboot oem lock
Once the install is done you'll have unlock the bootloader again using the token you already have from the first time, reflash CWM Recovery and re-root. All this will be 10x easier than the first time.
If you do re-root your phone, be 100% you backup the stock ROM in ClockworkMod Recovery before making changes!