Diagnosing a situation like that on pre-04 HD's is a major pain in the @$$ if you don't have a diagnostic computer. Basically, the check engine light comes on while riding and doesn't flash a code while doing a diagnostic check is a sign of a running only condition, then the code becomes a "stored" code that only a computer can diagnose.
I hate to tell you that this is a situation that only a shop can diagnose, but it is. SOME aftermarket shops have aftermarket handheld computers that can retrieve the stored codes, but not many, the computer is around $1500 and each cartridge for the different versions of HD's injection systems run around $500 each. So....your best bet is to simply take it to an HD dealer and have them plug it into HD's proprietary computer system called Digital Technician, they can retrieve the code and tell you what's wrong in a matter of a few minutes.
HD really made a smart move in 04 when they included a self-diagnosis system built in to the speedo. Retrieving codes from this system is easy as hell and along with the HD Electrical Diagnostics Manual, repairs can me made rather quickly and easily.
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