So here's the deal.  I have a 1989 GS500 which ran great up until about 2 years ago.  I started experiencing issues where as I was riding, the in-line fuel filter (yes the original owner installed one of those, which I can remove if people think it is unnecessary) would show no gas in it at all.  This obviously would cause the bike to start sputtering, and eventually just stall out.  After letting it sit for 15-20 minutes, the filter would be filled again, the bike would start right up, and after traveling about 5 minutes, same issue.  So, my initial course of action was to check all fuel lines, replace the outer petcock, and check the carbs to make sure everything was clear there.  Same problem occurred.  I then, for the heck of it, decided to keep the petcock in prime position and let gas just freely enter the filter without any sort of vacuum help, and the bike ran great.  Obviously there is an issue with the vacuum somewhere, but I didn't worry about it. Worked for about 6 months, no issues, then winter came, she sat for a bit, I started her every once in awhile, seemed to do fine, everything seemed good.  This summer, I took her out, didn't have any real issues until that same problem started to happen again, only this time, the petcock position is still in prime but she is still being starved of gas.  I honestly cannot figure this one out.  I rebuilt the carbs, replaced the fuel filter, I am just lost.  Any advice, or thoughts would be great! 

First, insure you have gas in the tank. I have seen it many times people think there is gas in the tank but it is just the remains in the bottom, which can look like a lot of gas.

Have you cleaned the frame petcock? They can get all gunked up with sludge from gas sitting in there.

Is the tank fuel valve on? Notch perfectly straight up and down?

If PRIME, if you disconnect the fuel line from petcock to carbs, does fuel come out?

Could the in-tank filter be all gunked up? (Look inside tank to see it. You might need a small mirror on a stock to see it or a spy scope.)

You do not need the in-line fuel filter.

Appreciate the very timely response.  I know there is gas in the tank as I filled her up haha.  Tomorrow when it is not so nasty out I'll check everything again and see if something is just gunked up in there or what not!

no teeny tiny splits in the fuel line?... no wet spots where there shouldnt be? ..

i know manufacturers like to do the minimum possible for cost saving .. but its always struck me as .. IF Suzuki had thought the gs needed an inline and replaceable cartridge fuel filter , then they most likely would have put one there eh? ..

ok i know there are always places that sell 'cruddier than normal' fuel .. but an inline filter just isnt set up for a gravity and low vaccum engine... mostly anyway ..

now someone gonna 'war' on me for dissing inline filters?... tell ya what .. i deliberately changed to e10 fuel too.... zero dramas thus far.... and thats with the bike sitting up to 4 weeks at a time!! .. 

Did you ever have the tank petcock off the bike? That can get clogged as well as the frame petcock getting clogged. I can't think of any other reason for gas not to flow from the tank into the fuel lines. This happened to me once on my other bike and I had to take the petcock off and blow air through all the holes/take it apart and de-gunk it with carb cleaner (gaskets off first of course). Have you checked if the lines are getting kinked in anyway?

It is very easy to pinch the fuel lines between the frame and the air box.

Sorry for the delay getting back.  We have had some nasty weather recently and I started a new job so I've been pretty busy.  I removed the inline fuel filter, checked the internal petcock, cleaned the carbs.  It seems to be stable for now...I am starting to think that the inline filter was absolutely the issue as you guys said the bike is gravity fed.  We'll see...hopefully I won't have to tear the bike apart AGAIN.  Thanks for all the information guys!

Yes if the inline filter was not designed for a gravity feed system then it will starve the motor..