Well from the lack of responses, either nobody is on here, or nobody minds a little documentation!
This has been a slow moving process, as expected, however, I have a friend that does this stuff for a living and he is more than willing to help me out, so hopefully I'll get farther next week. Anyway, here we go.
The first thing I did was to obtain a copy of IDA Pro 5.0. I have tried previous versions, but they don't support the HC16 chip that my car(2004 USDM WRX) has. There were some changes made and different years use different processors. Check the listings
http://forums.openecu.org/viewtopic.php?f=19&t=5 to see which one you'll need to support.
Once I had IDA Pro installed, I ran the program and chose File > Open. I selected a stock 04 WRX ROM(.hex) and selected the proper processor in the first pop-up box(Motorola 6816). I left everything else set as the default settings, and on the second pop-up box I left the defaults as well. Once the file had loaded, I hit "g" on the keyboard, which opened a prompt. This allowed me to chose an entry point(thanks merchgod!) so I entered 0x220 and hit enter. Once it was done with that I hit "c" on the keyboard which "unfolded" the ROM file.
I browsed through that for a bit, only to realize that I needed to do a lot more reading before I could understand anything. So I found the software manuals at the above link and dove into those. I decided the first thing I would do is try to memorize the commands, or at least get a better idea of what they do. So I made a spreadsheet(available upon request) with everything I found in the manuals. Not that that made things easy or anything, but eventually I'm sure it will help out.
Currently, I am waiting on some help from my friend to dive into things a bit more. I'm having a hard time with the locations of things, and how to follow the logic used. I will continue to post here though until I'm told to stop in case anyone ever decides they want to do this for themselves, as I have yet to find a "How-To" guide. Hopefully, it will help someone at some point.
If anyone has any suggestions, please offer them up!
Andy