Motorcycle Repair: CBR600rr Cranks but wont start., cbr600rr 04, honda cbr600rr

Question
I have a honda CBR600rr (04) and my battery was dying slowly so on a saturday morning i wanted to ride it. I went to start it and it wouldn't start so i figured that I would jump it wih the car. It worked breifly then died again. the Next day i tried again. this time i accadently hooked the battery up bakwards. OOPS. well i replaced the battery. and i believe that it is delivering fuel because I can smell it when i crank it over. I thout it was the CDI ECU (Brain) so i got one off of E-bay put it in and still no luck. But with the new CDI box my bike flashed a code at me 2 long flashes and 3 short flashes. What do you think the problem is. Could it be the plugs. and also does the number on the cdi box have to match. I have been told that the one i purchased works on 03-05 cbr's ? but others have told me that i need to fing the exact one. I hope you can help me  

Answer
Hi Randy,

A little past tense, but never use a car/truck battery to boost start a MC engine. The current is much higher in the car/truck batteries and will harm the electronics, as you seem to know.

First thing to do is check the spark plugs. They may have become wet fouled by fuel during starting attempts.

Next, check for an arc at the spark plugs. Keep all plugs grounded to the engine of chasis ground during testing to avoid damaging electronics.

Honda's CDI/ECU part numbers should be same. Ignition
characteristics are unique to each MC engine. You may see an arc at the plugs with any CDI that fits the multi-connector, but timing/firing order may not be correct.

I don't have access to the trouble codes definitions anymore.

Fuel should be fine providing the MC was not stored or the fuel is not older than 3-4 weeks.

Respectfully,
Mark Shively