The project is back together, but I'm having problems adjusting the air screws. I put 40 pilots and 150 mains in, put two #4 washers on the needles, turned the air screws out three turns, and installed a K&N drop in filter without the restrictor. Last night I fired it up for the first time. It started right up cold and ran without any help, though there was some coughing and sputtering as if it were running rich. I played with the air screws and rode it around a bit. It backfired going downhill and coughed and sputtered with no power going uphill. I  gave up for the night as it was getting dark and tried again this morning. Now I can't even get it to start regardless of where I position the air screws. Starter fluid just makes it cough and sputter for a couple of seconds, then die. Choking it makes no difference either. I live at 1200 ft. above sea level. It's 40 degrees outside. We had a full moon a couple nights ago. Where should I go from here? Should I try the 140s, or does it sound bad enough to go down to 127.5?

Ok, I got it running, but rough. Something wierd is that loosening the left air screw increases the rpms (to a point), but loosening the right one does nothing. TIGHTENING the right one actually increases the rpms a little bit, right before it seats all the way down. I loosened the left air screw until the rpms quit increasing plus a quarter turn, then put the right one in the same position. When I rode it, it would sputter when I first released the clutch, then pull for a bit, then start sputtering and lose power at higher rpms. It barely had enough power to climb the hill back to my house. I loosened the air screws one turn, rode it with the same result, then loosened another turn with the same result. I tried tightening and riding with the same results.
I think I'm going to try 127.5 mains first. It's very rich. I'll post up what happens.

Now I have the 127.5 mains in. It runs much better. There is no coughing or sputtering when I ride. However, it is grossly underpowered. I almost didn't make it back up the hill. Adjusting the air screws doesn't seem to help.

The air screws are for idle mixture only.  They do nothing off idle.

You shouldn't need 150 mains unless you have a Vance and Hines full exhaust. 

Stock size is somewhere around 127.5 on the 49 state version as I recall.  Do a quick search in the FAQ for the "Jetting Matrix".  That will  help you get a baseline on your specific combination. 

From there, do a few plug chops to get things dialed in.  Ride along at a given RPM for several miles, then hit the kill switch as you pull in the clutch.  Pull a plug and have a look.  Light gray to light brown soot on the insulator nose and grounding electrode is what you're looking for. 

You can also get a pretty good idea of your jetting by using the throttle, assuming your slides are correctly compensated.  Some people take nylon screws and block off the compensation ports in the underside of the slides.  The GS will stumble badly between 4,000 and 5,500 with all four ports blocked. 

For a full run-down of the procedure for jetting a CV carb, check here:

http://www.factorypro.com/tech_tuning_procedures/tuning_carbtune,CV,high_rpm_engines.html

Let us know how things work out.   

It's been my experience with dirt bikes that if you are able to close off the air bleed screw for the idle mixture and it has no effect on the engine, it means either the pilot jet is plugged or the jet is way too big and thus has enough fuel to keep the engine running no matter where you have the screw positioned.

Check ALL the vents/orifices in the carbs and make sure they are all clear.  Also make sure that you have not accidentally places the mid jet and main jet in the wrong holes (main jet screws into the brass extender and the mid main goes to the bottom left of the main jet, next to the pilot jet)

I'd also make sure that there aren't any leaks in the rubber intake boots that lead from the cylinders to the carburetors.  No amount of carb tuning will be able to get the bike running properly with cracked intake boots.  Also check for any other sources of leaks in the carbs such as vacuum diaphragms and such

Hope this helps, good luck!

Thanks,
Josh