starting mystery

i've recently aquired an 86 kzp1000 and have been benefitting immensely from reading the archives here. i thought i was pretty handy with a wrench but i've come up against a stumper that's about to make me cry.
the history:
starter clutch was making a horrible clunking/rattling noise. hoping it was just bad timing, i parked in the driveway, ran the bike and checked the timing on both coils. both were dead on. i turned the bike off and opened up the generator side. after much fighting, cursing, trips to the hardware store and more cursing, i got the rotor off (btw - filling the #1 cylinder with a rope on the compression stroke to lock up the motor for removing bolt - awesome tip, thanks, putting a ball bearing in before the back axle/puller? not so awesome (spent a whole day trying to get the bearing out of the end of my crank)). sure enough, two of the three allen heads holding the starter clutch to the rotor were snapped in two.
i also during this time dumped a half a bottle of fuel system cleaner in the tank, thinking i would be up and running soon.
so, after waiting for three new bolts and a copper washer to be sent over from japan, i reassembled everything and pushed start. it just cranked and cranked, but wouldn't fire.
i finally pulled the carbs to give them a real cleaning and found them to be a little crusty but with no plugged jets or obvious defects. i found huge deposits of rust flakes upstream of the needle seat on both outboard carbs. thoroughly cleaned, i buttoned them back up, checked the action on the needle valves and the slides and they seemed to be operating perfectly.
mounted the carbs (with fuel filter) and still no dice. checked the spark again at all four plugs - fat and blue. did a finger-in-the-hole compression test and it was good. checked all the vaccum lines. drained out all the gas and replaced it with fresh. cleaned and checked the plugs again. they were a little wet from cranking, but not flooded. let the bike sit a few days, charged the battery, still nothing.
the bike was running fine, i replaced the starter clutch bolts, and it quit running. what could i be missing? one last clue (but it could be a red herring) the starter won't crank when the battery is below 12 volts.
irrelevant, right? if there's spark, there's spark.
thanks for reading such a long one. now i'm going to go cry. any help appreciated.

How did you check timing to the coils? Your bike has an electronic ignition and timing isn't alterable. Did you check voltage going to the coils? If this were my bike, I believe I would do a full tune up per the factory service manual. You are doing some of the right things but didn't mention checking valve clearances (hard starting? there is a good reason!) and the carbs may have to be cleaned more thoroughly. If it isn't starting, the enrichener circuit is likely plugged up on one or more carb.

Try starter fluid. That would of been my last option. Is gas going into the carbs? Did you prime the carbs, O wait you did say the plugs were wet. Try it without choke!

when i say i checked the timing on both coils, i mean i hooked the timing light up to cylinder 4 (1-4 coil) and then 3 (2-3 coil). i know there's no adjustment, but ignitions fail, right?
i don't feel like valve clearance could have changed drastically enough to keep the bike from running since i didn't really do any mechanical work.
i guess it could be the enrichment circuit. i'm assuming that's those tiny little holes on the top of the venturi right after the throttle plate? is there a method to clean them besides blasting them with carb cleaner? i seemed to get more of it in my eye than in those little holes.

well everyone, i finally figured it out. the reason i couldn't get the carbs to work was because they weren't the problem. in all my monkeying to get the rotor and starter clutch off, i managed to loosen the bolt on the other end of the crankshaft that holds the ignition advancer on. unbeknownst to me, the advancer pivoted on the shaft before i tightened it back. thus, when looking only at the points (i know, it's electronic), the bike seemed to be timed properly, but, when compared with the action of the valves, the bike was firing somewhere in the middle of the exhaust stroke.
so, the lesson here? who knows. never make assumptions, i guess. now if i could just get the damn starter clutch to stay tight to the rotor....