I have a 2000 GS500.   It was running poorly (regular high rev sticky) and has for a long time so last fall I did the jetting swap out.   It worked great and the bike fired up and after warm up returned nicely to Idle.   

I drained the carbs, and put it to bed for the winter.   Fired it up a couple of weeks ago.  It took a touch of ether to fire the first time, but then it ran fine.    After a couple of days it got cold so I decided to balance the carbs.   (mercury manometer connected to the nipples on the carb body.)

During the balancing the bike started running worse and quit.    I could not get it fired up again.

I figured that I butchered the balancing so I took the carbs off and did a bench balancing with a piece of guitar wire.   Put it back together and it still would not fire.

I noticed that the right carb was not getting gas so I took them off and cleaned everything again.   This time I put in an inline fuel filter and tried to fire it up.   Nothing.   

It will start on ether but will not draw gas.   I have checked spark, I have checked that there is fuel in the bowls.   I am not sure where to go next.   

Any suggestions?

Have you checked your air/fuel screws? Vacuum hoses?

I took out and cleaned both air mix screws, re-set it to 2.75 turns.   The vacuum that opens the petcock I plugged with a dowel and the second vacuum port has the rubber nipple on it.  ( i have not checked the nipple for holes.... but it seemed fine when I put it on)

You did have it on prime while balancing right. You plugged the vacuum line so petcock won't open if you did...

I don't think it's related to the bike not starting at all, but I had a problem where my bike would run poorly and no amount of adjusting the A/F ratio or attempting to balance would remedy it.  Turned out my valve clearances were out of spec.  Once I adjusted valve clearances I was able to balance the carbs and the bike ran MUCH better.  Once you get the bike to at least start it might be worth checking.

Did you check the float heights? mine was doing something similar, float heights and bench sync got it pretty good, close enough to sync with the mono.

I might have sync'd with the prime on.   But I am now running fuel directly into the carbs so that should not be the problem.

I have not checked the valve clearance.. probably should but it was running fine prior to me getting the great idea to balance the carbs.

I have not checked the float height.  I will do that and see what happens.

Joester41 nailed it.   I adjusted the floats and it fired right up.   Nice.  Thank you all for giving your suggestions this forum rocks.

Iver.