i have a 2002 gs500 and the engine seized so i put a 2004 motor in it. everything is hooked up but it wont run. sort of sputters and tries to start but wont. i have spark and fuel, but the timing is off somehow. i took it to a suzuki dealer and they looked it over and told me the ignition box would need to be changed. (for $500) I changed the signal generator plate and diodes, off the 02 engine onto the 04. from what i have seen that was the right thing to do.i need to know that if i change the box if i have to change the wiring harness too. if anyone has been in the same situation or races these bikes and knows firsthand what modifications need to be made when swapping motors, i would really appreciate some advice.

02 ignition advancer may have to be put in place of the 04's.
The ignition box ... yea sounds like they want to make 300 bucks dealer mark up, 200 bucks labor to swap it (obviously they have to get to it, its all the way under the left side cover. 3-4 screws and 2-3 grommets have to be removed) and still leave you with a POS that dont run.
I am just guessing, but ignition advancers are different from 02-04.
Cool.
Buddha.

I would swap all the electrics from the old motor to the new motor.  is the motor turning over but not firing? is it getting fuel?  are you sure the motor you bought was good?