I downloaded a game and removed a Trojan virus that was inside of a homebrew game. I foolishly converted to ISO and burned to a dvd r-. The most stupid (Or at least I think) thing is that I copied the homebrew game to my hard drive. I don't know if my mod chip needs to be resoldered or if I need a new hard drive. How can I tell what the problem is?

I'm not sure I understand. You believe you have installed an xbox trojan and it has done physical damage to your modchip or hard drive?

I am not sure. How can I find out?

I am quite sure there is no trojan installed on your xbox. Anything is possible but that would be somewhat difficult to create and I doubt anyone with those skills would wish to bother.

What can I do to make it stop freezing?

Maybe console is overheating?

How can I make it not overheat.

Put new thermal grease under GPU and CPU heatsinks and you can replace original fan with 80mm PC fan. It will be much quieter.

Is there a tutorial somewhere for doing this?

Yes.
http://www.xboxscene.com/articles/thermal-compound.php

But firstly check temperatures in your dash (XBMC, Evox, UnleashX).
After an hour of game CPU temp shuoldn't be higher than 60C.

I can't because it freezes right when the bios finishes.

Can you boot an xbox game?

My Xbox has stopped freezing.