The most, if not all of them are in engine.dll
When you find the commands you'll notice that all of the patched ones (atleast that I know of) are in order after a "Key Error" line or something to that effect, I'd like to get a second opinion on that after you have a look.
I found a few in client and server, but I don't think they were very relevant.
I'm using IDA for a decompiler, OllyDbg is another option.
Thanks to Nico on that ^.^