i just bought a 95 gs 500 i rode it home and it would idle at about 3000 rpms after it was warmed up about 15 minutes of easy riding. I took it home and tore the carbs apart and cleaned them. ive also just barley had the valves redone but now it will only start and idle with the choke all the way on and it will not throttle up without dying. it dies almost instantly when i turn the choke off. Anybody have any ideas on how i can fix this?

Need pic!  I'd also use the 'search' feature as there are pages and pages of info available here. 

First thing to check after rebuilding the carbs is the height of the gas in the bowls.  This is adjusted by bending the little tab above the float needle.  It is checked by attacking a clear aquarium line tube to the drain in a U shape and opening the drain.  The gas level in the clear tube should be level with the float bowl gasket.  Check that and then get back to us.

As far as the hanging RPMs, that could have been caused by an air leak in the carbs, or simply because the idle screw is screwed in too far.

There are two small o-rings at the top of the carbs (one each), under the carb covers. If these are missing, or the wrong size, your sliders won't work as expected and you will have hanging idle.

Not the only cause for hanging idle, but a fairly easy one to miss...

so i did the clear line thing to check the floats and the gas stays right where it should be. the o rings are there so maybe its an airleak how would i check for that?

do i need to put the air box and gas tank on ive been using a funnel that i connect to the gas line so maybe its just a simple vaccum leak?

You do need the air box  on with an air filter. It restricts the air flow to what it should be. No airbox = hanging idle.
Fuel is OK through anything. If your fuel us much higher than the true tank position, gravity can force too much fuel in and the float needles will not be able to control the fuel flow.

does anyone know where i should set the idle, carb sync screw, and the air/fuel mixture at? keep in mind i live in utah so my altitude is higher then most

Not trying to be a jerk, but the 'search' function is a good feature of this forum.  Where's Twisted when you need him,....

Check the forum wiki, off the top of my head i believe it's wiki.gstwins.com

ive tried the search and i havent had much luck but i was looking at my carbs and noticed that the air passage jet in the inlets(where the airbox connects to the carb) are completely stripped does anybody have a trick for getting them out.

I ordered this EZ-out from McMaster-Carr:

http://www.mcmaster.com/#catalog/118/2851/=ig5b76
P/N 2563A11 - Screw Extractor, #1, for #8-1/4" (2.5-6MM) Screw, Bolt, & Stud

I had the same thing happen to my carbs, and I had a machine shop drill it out.  I wish I would have done it myself and used the screw extractor, because they drilled out a lot of the threads too.  I had the same thing happen on a set of carbs that I got used, and I used the EZ-OUT with perfect success.  You just have to 5/64" drill bit first to start the EZ-Out.