I had the same issue when I woke up yesterday. This is what i did. I am also new at rooting but with reading on here I got the phone working.
First thing I did was clear the cache.
Then when the phone booted up and it asked me to update, I rejected.
I downloaded MyBackupPro from App store ($2.99) and backed up my phone's apps and data on the net.
I copied all my pictures and videos to my computer.
Idownloaded ROM Manager from AppStor, was free, to flash the ROM.
I used this tutorial from youtube on how to flash the rom.
How to Install Custom Roms Onto The HTC Thunderbolt - YouTube
I used the second method that starts at 2:22.
The ROM I used is the one that Jrocker23 provided from his website:
**UPDATED 12-19-2011** Ginger BreadRock V3.0 & 3.1 AVAILABLE NOW - HTC Thunderbolt
Jrocker23 has2 ROMS, a full rooted version of the update Version3.0 or a stripped down rooted version with no Verizon crapware Version3.1 (that's the one I used).
After the new V3.1 was installed. i downloaded the new radios (also from JRocker23 website) and used this youtube video on how to install them
How To Flash Radios To The HTC Thunderbolt - YouTube
After that I had a workingTB with the new updates. The phone was like new and everything was wiped. I redownloaed the MybackupPro APP and restored all my Apps and data that I had saved earlier and bam, everything is good to go. Thanks JRocker23 for the ROM and radio.