I have a 2004 GS500F that I am having problems with. 

Let me start from the beginning. Before winter hit I did an oil change on the bike. When I did that I didn't notice that the bike was on an incline when I was adding the oil, so I didn't realize I overfilled. When I went to ride the bike after that oil change it died in the middle of the street and would not start back up. So I got the bike back home and put new spark plugs in it and it started up fine. However when I started it up there was a metal on metal sound coming from the engine. After tearing it apart I found that the three bolts holding the starter clutch to the generator rotor had sheared off...no big deal. So i replaced the bolts, put it back together no problem.

Now on to the current problem. After repairing the starter clutch I tried to start the bike, but this time the engine would crank but not turn over. Spark plugs are good, so I figure it has to be a fuel issue. So I pull out the carbs, do a good cleaning on them, and put them back in.  This time I am able to get the bike running.  After about 5 min of it running it shuts down on its own, and now won't start back up.  Pull the spark plugs out and they are drenched with gas, as is the air box flooded with about 1/4 inch of gas.  To figure out why the engine is flooding i pull the carbs back out and check the float height and make sure the needle valve is sealing.  After doing the inspection everything looks perfect in the carbs.  So i put them back on, and after letting the gas in the engine evaporate away over night I try to start it again.  Still with no results.  Now the engine wont even start with starter fluid.  When I pull the spark plugs back out they are saturated again with a little bit of gas, but not too bad. So i'm not sure if the engine is still flooding. Also when I crank the engine after a few seconds I can see gas vapors coming back into the air box. 

Myself (relatively new to vehicle repair) and my dad (who restores and repairs cars as a hobby) are stumped.  we have compression, we have spark, so really all thats left is a fuel issue.  Any thoughts or ideas would be greatly appreciated because we are almost at the point to bring the bike to the mechanic, and I don't want to have to spend the money for that.

I'm hoping someone with more knowledge than I of these carbs might come on here, I've never had mine apart.
Seems like the problem might have been a flooding carb due to dirt in the needle/seat, then you pulled the carbs apart and now it won't run. So I'd suspect something might have gone wrong in the reassembly of the carbs. Do you have a manual? I'd be checking that everything went together the right way, all o-rings are in there, needle clip is in right position re slide and spring etc etc. Certainly seems like its getting too much fuel, and that would stop it running on the starter fluid.
Like you say, if you've got compression and a good spark it should go, which leaves fuel....

Maybe try turning fuel tap off, drain the carbs, then try the starter fluid or a fine mist of fuel in the intake. If it fires, you've narrowed down the problem to too much fuel.

It's also possible that you badly damaged the valves when overflooding the cylinders with gas.  If your petcock leaks or your float bowls overflow and gas gets into the cylinder, it can cause damage on the compression stroke.  Other folks might know more about this effect and can offer some tips on how to test for it....

QuoteIt's also possible that you badly damaged the valves when overflooding the cylinders with gas.

Next time I get a change I am going to take the valve cover off just to check this.  Also I could be wrong, but if the valves are damaged isn't it true that I shouldn't be getting any compression?