Both radios are leaked versions. The Official Verizon OTA hasn't been released yet. The only difference between the two is that one is for rooted users and one is for stock users. You can not flash the MR2 RUU radio on a rooted phone running Froyo or you run into the chance of bricking it. The MR2 radio for rooted users will only work on Gingerbread roms (or CM7) for now
* until the Official radio is released by Verizon.
* Reason: The leaked radio for the new Froyo OTA uses the new RIL, which was previously incorporated into the GB leak but not in the older Froyo releases. Thus, it works on the current GB roms but not on Froyo roms.
http://forum.androidcentral.com/thu...-backup-restore-install-roms-thunderbolt.html
As for Installing/flashing roms, the guide in the sticky will walk you through the process step by step. There's also a full list of roms, radios & kernels available for the Thunderbolt in the third post. If you have any questions or need further help.. post it over in the guide thread and I or someone else will help you out.
Flashing radios:
1) Download the radio file
2) If not already done... rename the file to PG05IMG (pg zero five img).
3) Place the PG05IMG.zip on the root of the phones SD Card (don't place it in any sub-folders)
4) Power your phone into hboot/bootloader.. (turn the phone off.. turn the phone back on by holding the power button and the volume down button at the same time until your phone starts up in hboot/bootloader).
5) You will be asked if you would like to install the zip.. choose YES with the volume up button.
6) The phone will take over from there and begin to unload the PG05IMG.zip onto your phone.
7) When completed you will be asked to reboot the phone.. choose YES.
8) You're done.
*delete or move the PG05IMG.zip from the root of the SD Card. (If not, you can run into some problems if you ever need to get to Recovery from hboot/bootloader*
I'll add this info to the Guide when I get a chance for anyone else that needs it.