If it has an aftermarket Fuel Injection programmer (like a dynojet powercommander), it may have lost its programming. Some of the older systems used a serial connection to upload/save FI programming...some newer ones use USB. You would need to identify if you have one - what model it is - then determine what map it needs and upload accordingly.
Sometimes the FI on the bike needs a reset or determine the code being generated. Here is a forum that lists the procedure:
http://www.fireblades.org/forums/articles-honda-fireblade/100273-2000-cbr929rr-fi-light-red-light-please-help.html
Good Luck.
SOURCE: Bogging and stalling at high RPM's
The main jet need cleaning.(you should clean them all though)
Main Jet: Main jet comes into play at three-quarters open to full throttle conditions. CRITICAL to high-speed engine operation. Not only does it meter the gas into the engine, it can aid in cooling the engine as well.
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SOURCE: just bought a honda cr 100, yes i got it started
Your timing is off. Try backing the timing up to 4 degrees before top dead center!
SOURCE: should my 03 honda cbr 954 stay running after I
The altenator combined with regulator should keep the engine running without a battery. It may run a bit lumpy but it should run.
You have either a regulator or an alternator fault.
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