Yep. If the part numbers are different on the 98 and 03 (which they probably are) it won't work.. no matter what you flash it to.
Have you tried to flash an 04 BIN file on it?
I have a power tuner and could swing by this weekend and try that if you want.
Have you tried scanning the car for codes? Even if it doesn't start it should throw some codes if its in the PCM.