This post is more for my own benefit than anyone else's; every time I fire up IDA Pro with a fresh ROM, I have to re-learn how exactly to get to a usable disassembled image.
Assuming you have an ECU image from your car saved as a .hex with EcuFlash, fire up IDA Pro (I'm currently using 5.0.0.879, so this might differ from version to version), and go to "File" and "Open...". Select the "Hitachi SH4B" processor from the drop-down, and just keep clicking OK until you're presented with the ROM view.
The first four bytes of the ROM tell the processor where to jump to when booting; so, type "g", and enter the address stored in those first four bytes and hit OK. Then, type "c", and watch as IDA Pro disassembles your code automatically in front of you.
After that, though, you're on your own. See AktiveMatrix for the latest in what people are doing with a disassembled Evo ECU, as well as the forums at OSEcu Roms and OpenECU.