I think there may be a safer way.
1) Backup everything. Make a NANDroid and make backups in TB/Mybackup Pro/whatever. You will end up wiping data, and NANDroids are always good.
2) Lock your bootloader - this step may be unnecessary, you can try step 3 and see if it will let you apply it without locking.
3) Apply the latest RUU file (
xda-developers - View Single Post - [ROM] STOCK 2.17.651.5 Update.zip + Radio/Firmware bits) - This wipes data
4) Re-unlock your bootloader (if you locked it)
5) Go to
[ROM] STOCK 2.17.651.5 Update.zip + Radio/Firmware bits - xda-developers. Under the image of the OTA message, there are two ROMs you can download. One is very close to stock, the other is a deodexed version. If you just want stock + root, take the top one. If it doesn't matter to you, take the top one.
6) If you take the top one, make sure to get the FULL boot.img kernel in the pair of links below. If you picked deodexed, you can take the second one.
7) Wipe Cache and Dalvik cache. Wipe data if you want to be absolutely sure everything is clean, but it's not necessary.
8) Flash the ROM and Kernel in fastboot, like you would any other ROM with HBOOT 1.5
That should end up with no bootlooping. I'd hope. <crosses fingers> I really, really hate HBOOT 1.5. I kinda want to buy a used Evo 3D to just put on HBOOT 1.5 and figure this stuff out.