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As a suggestion moving forward, things like this should not be done in private. It's much more beneficial to the entire community to play it out on a forum. The reason i say that is, look up .... more people have the exact same question and because this played out behind closed doors, they have no answers.
To answer the questions. The "bloat" is stored in a directory called /system. More specifically /system/app. As a normal user you only have r/o privileges to this directory which means you can't edit anything. To explain a little better for the windows guys, rooting your phone makes you the admin of your machine. So to become the admin of your machine aka your phone, you need to root. The trick with HTC phones is you also need to unlock NAND, not just root.
Once you're rooted with an unlocked NAND, you can use ADB to access /system or pony up a couple of bucks for an amazing app in the market called "Root Explorer". What root explorer does is allows those with rooted phones to mount r/w permission on the /system directory. This can be done on the fly without a PC.
Ok so you've rooted, you've got Root explorer, when you opened it you gave it root permissions .... whats next? Simple.
Go to the "system" directory, then go to the "app" directory. Now your faced with a bunch of apk files each with a matching odex file. These are what needs to be removed to remove an app. Inside of system/app directory in root explorer, look at the top of the screen and you'll see a button that you can click to mount as r/w, click that. You now have r/w on system and can remove apk's and odex files
HERE IS A WARNING - Do not just go willy nilly removing stuff!!!!!! you will break something, you will regret it, you will then probably require someone to help you get back up and working again.
EDIT - HERE is the guide i wrote for the EVO guys back when i had an EVO. The concept should be similar if not the same. Please read it and feel free to copy and use it in any fashion you want and modify it to suit the Thunderbolt.
EDIT #2 - Some dude named Cory Streater (Hey Cory!) made perfect instructions for you guys.