OK, need some insite.

[hawaiianGS]

Quick back story. I have a 2000 GS. It is currently sitting at 15,000 miles. Last week I started out to go to work, and was greeted with, Chug a Chuga, pop, pop. Seemed to not be getting fuel after warming up for about 5 minutes. It did this in 1st-3rd gears. The rpm's would not go past 4,500. I turned around and took it home as I didn't have time to work on it. My first thought was the carbs. After work I switched the plugs just to make sure one wasn't faulty. No change. Pulled and cleaned the carbs. Original jets on both sides. The carbs were not too bad, but I cleaned them, then put it back together. The air filter was clean and the air box empty. I put in new plugs, properly gapped, just to be safe. It idled better and ran better. Forgot to mention the left plug looked great, the right was running a little rich. Once it was back together took it for a ride and it seemed fine. A little weak but fine. I rode it for a couple days, and then it started again. No power at take off. In fact full throttle would put it at about 4000 rpms, until I drove for 10-15 minutes. After driving for 10-15 minutes it would then run fine. Great in fact. However, if it sat for an hour, it would run like garbage again until it ran for a while. It almost seemed like hitting bumps would loosen up something and then it was fine. Anyway, I pulled the left plug while it idled and the engine shut right off. If I pull the right plug it continues to run. OK, valves maybe? I checked the valves today, (thanks baltimoreGS, great vid) and all seems good. .04 on both intakes, .08 on both exhausts. I didn't change the coils or synch the carbs as I ran out of day light. I did ensure both mixture screws were Set 2.5 turns out. The battery is new and the plug wires are good.on the way home today it started doing the same thing again. WOT put me at about 4500 rpm.pulled the plugs to check. The right one was a little rich still and the left looked brand new. It isn't firing at all. Checked compression with my thumb, I know get a gauge, but it seemed fine. Left still isn't firing though. Any ideas?  Kinda wordy I know, sorry.

[hawaiianGS]

Forgot to mention, it does the same thing on prime,reserve, and run petcock positions.

[Big Rich]

I can't remember - which carb does the fuel line run to? Maybe there's a partial blockage or something preventing your left carb from getting enough gas. Or even a sticking float?

And check that both slides are moving up and down freely and at the same time (airbox off and motor running of course).

That's all I can think of at 4am........

[SS Adrenaline]

Sometime the float gets stuck closed.  Just take a screw driver and knock on the side of the carb that you think isnt working.  If it works then you need fix the sticking float.

[jestercinti]

Hitting bumps and having the bike run fine sounds like either float problems or ignition/electrical related.  Try checking all connections.  Start at the battery, move to the ignition pickup, then to the coils, then to the plugs.  I once had a bad connection on the harness from the ignition pickup to the coils.  If I touched it, the bike would run very erratic/die.  Took me 3 days to find this out.  Same symptoms.

If you confirm it's not fuel/float related, try tracing the ignition system.  Worth a shot.  Loose/bad connections will drive you crazy.

[pliskin]

I had a bike that did that (not my GS). It was the gas cap. There was a little BB valve that was sticking causing a vacuum to build and starving the motor of gas. Sometimes I could just give the cap a whack and it would open up. Sometimes I had to open/close it.