Hello friends. Let me give you the breakdown of my problem:
I brought my bike into the dealership to get my rear shock and front spring put on. The bike doesn't stay idling at all and I wanted them to take a look at it. I brought it to them a few months ago cause of starting problems and they cleaned the carbs out. The bike ran fine for awhile until the last month or so where it will always dies unless I give it a little throttle. Anyway turns out bike is only running on on cylinder,(they said something about 100% leak). Anyway the valves we super tight and they said they moved quite a bit. I got new shims in it and they valves are back in spec, but one cylinder is still not running. They can't seem to figure it out.

So anyway all that work cost me 600$ and the bike is pretty much the same. They also said there was so much movement they could not guarantee the valves would stay where they should.

Bike is a 2004 GS500F with 17k miles. I bought it used at 9k miles.
I have been running it on one cylinder apparently for awhile. Attempting to fix the problem with the dealer is going to be a 1300$ job. I really don't want to do it without a second opinion. Its a Yamaha dealership but they have serviced the bike before. The guy recommended selling it but I don't think anyone will want to buy it in this condition. I'm in the Sacramento, CA area and would like some recommendations on another place I can bring it. If anyway around here wants to take a look please feel free, I'm willing to pay as well.

I've searched the forums as well, read some possible problems, but I don't have any experience so I don't know where to start.

Suck, squeeze, blow.  Air, fuel and spark are needed in any internal combustion engine to run.  Do a compression test first.  If your bike has compression then you know the mechanical side of things is good (shows your valves are doing their thing).  Then you are left with air/fuel and spark.  If you have a spark plug laying around, hook it up to each of your spark plug wires and hold the tip against the engine while you run the starter motor and look for a blue arc (spark).  Then you are left with air/fuel which would mean pulling the carbs and cleaning them.  Good luck!  
 
-Jessie

Is your gas mileage really low on one cylinder?  How do the plugs look?

Post your location, and the pics of the beer you'd offer to any knowledgeable gstwinner who volunteers to come over and check it out.

$1300 will net you nothing from geniuses who dont diagnose the problem first.

And jessie - you forgot Bang  most important part.

Cool.
Buddha.

Updates!

So I just picked it up from the dealership today. And even though the right cylinder has a "85%" leak its managing to fire. The mechanic said he didn't know how(lol?). I could definitely feel the difference. And it now idles with no problems. Can't believe I was riding it with only one cylinder for so long. Anyway I'm not sure what to do from here. The dealership says it most likely won't stay running like this for long. They recommend selling it

To answer some questions. Yes I was getting horrible gas mileage before, 30-35 mpg. Haven't had a chance to ride a whole tank yet. Will test.
I had the carbs cleaned not too long ago. I'll check the spark plugs.

Some other things: I was going to have them replace chain and sprockets, my chain is loose and grinds on the top of the swing arm when I come off the throttle. I keep tightening but it gets loose anyway. They said it wasn't worth it so I'm still running on that. Also when I checked my K&N drop in filter it had like gasoline on it, this was prior to bringing it to the dealer. I cleaned it off, its not supposed to be like that is it?

So at the end of this day I have a bike that runs great but still needs work. Minor or Major I'm not sure. I have .85 sonic springs and a kat 600 rear just lying around right now .

Location is Lincoln, CA 95648, around Sacramento. Again if any of you know a place I should take it let me know. Will gladly pick up some beer if required as payment.

gas on the filter is because your floats are set to high and gas is running up and out the jets and back into the filter and forward into the cylinder, running down the walls and in the case

smell your oil, probably change it and reset your float heights

Right on the floats skirecs, and the overflowing cyl can have oild wash, and hence be dry @ startup and hence have more wear.

I used to live in sac - the greenhaven area, and I'd say @ that time the only 1/2 decent mechanic worked @ Cycle gear.
I actually dynoed my GS @ chandelle motorsports, and those guys, and jody matsler next door to chandelle and lee who was Jody's biz partner were all into racing GS'es.

Anyway, I dont know any of em now, this was all 12 years ago.

85% leaking - or you have 85% pressure on leakdown test ... that isn't too bad considering they do it cold. I would ride it, I dont see it being anythign you can fix without major rebuild ... But fix that float and see what that does.
Cool.
Buddha.

Hey all just wanted to give some up dates.

Took it to a much better mechanic. Compression Test was done and it was perfect. Turns out the gas on filter was cause I was overfilling the gas tank lol ><. The chain is getting stretched and I'm going to have to replace it in a couple thousand miles. Overall everything seems fine. I had the rear shock replaced with a kata 600 and some sonic springs put on the front. I must say its very stiff, but it handles beautifully in the turns.

Glad you're getting it sorted out   

-Jessie