So what size jets did you order?

mjn12, I just sent you an e-mail with my info 

Chris_B, READ HIS LAST POST 

Ducati - you got the pilots when they come. I replied to your email as well.

I was told by multiple people that it was possibly a result of running lean, However, it doesn't seem I can make it run rich. I figured a rejet couldn't hurt.

So far I have:

Cleaned carbs
Adjusted Float levels
Adjusted mixture screw
adjusted idle
confirmed choke is not sticking
Checked for vacuum leaks at carb boots
Checked for vacuum leaks at inlets

I have yet to check valve clearances but I'll probably do that when I go home or maybe this weekend (its nice out, I really want to ride).
I'm also gonna order a new o-ring or two from bike banit since partsnmore is out of rebuild kits and replace anythign in there I considered iffy.
Once i know valves are in spec all I can do is balance and hope somewhere along the way my problems are solved. Otherwise I'll have to throw in the towel and get
either a dealer or my much more knowledgeable uncle to help me when I move back to ohio in december.

Cool, I'll finally take care of the bogging in the midrange with those jets, thanks 
As for your problem, it sounds like you've checked everything but the valves, which I've thought was the most likely culprit from the begining. Pay special attention to the intake valves, and even if they are within spec (doubtfull) but at the minimum clearance, try opening them up to middle or upper end of the clearance range to ensure that the valves are fully closing.

Some may disagree with me but you can remove the shims and sand them down. Just get some 600 grit wet sandpaper, and wetsand the bottom of the shim. Place the sandpaper on a piece of glass to make sure that it stays flat and you should be fine.

Also, you only need feeler gauges to check the clearances but you need a special tool to remove the shims. I've found an inexpensive place to order them here
http://www.pitposse.com/vaadto.html  it's the $18.90 one.

Have you checked your compression yet?
Hope this helps
good luck 

I have not checked compression yet.  That was going to be my next step after the valve clearances.

Compression testers I've seen online seem to be running upwards of $100 in cost, definately not in my range.  I have to get the bike inspected for registration within the next 10 days so maybe when the shop is inspecting I can have them check that real quick for me.

rent it form advance  or auto zone

I was going to recomend doing the compression test to tell you if the valve is leaking or not. If you can't get your hands on one easily and cheaply don't worry about it, just check the valve clearances. If the clearances are off then you know you had low compression. If you adjust the valve clearances and it solves your problem, your compression is probally just fine.

Have you checked those valves yet? If you have the feeler gauges, it only takes about two hours if it's your first time. No biggie.
Good luck 

I've got the feeler gauges and the telescoping magnetic picker-upper dealy (is there a more technical name ).  As soon as the tool for depressing the buckets shows up from pit posse I'll check those clearances.  I'm betting theyll be off and I don't feel like tearing into it once to find that out and again in 5 days when the tool shows up so I can pull them out and order some new ones. The dealer where I'm getting the jets stocks most sizes of shims so when the jets show up I can probably just get everything at once.  The dealer is half an hour drive from me and I want to fight my way back home through D.C. rush hour traffic as few times as possible.

Cool 

you can get a compression tester for ~$20 from walmart or ~$30 from Sears.  Or, as rangerbrown suggested, you can rent one from a major autopart store.

Checking the compression is something you'd do before checking the valves.  If the valves are tight, then you'll have low compression, and checking compression is A LOT easier than checking the valves.  If compression is with in spec, then it's not your valves or head gasket or rings or anything like that.  But if you're checking your valves anyway, I guess it doesn't really matter.

$20 at walmart sounds good,

Will i need to find one to fit the spark plug holes on the GS? If so what size?

Edit: Nevermind, spoke before I searched. Its 12mm.   I got roped into playing tennis tonight so no time for the GS. Thursday I'm supposed to be at the gym... maybe I'll just have to skip that.

I checked my cleanances, the intakes were off by as much as .1mm (I went from 2.65 to a 2.55), one of the exhausts was ok and the other was only .5 off.  However, I have to make the 40 minute trek to the dealer to pick up another shim.  The guy there first told me the shims were a buck a piece, so I was gonna pick up about 10 of em in some various sizes since I didn't want to have to make that trek again and I had zero clearance on all the valves that were off so I couldn't figure out what size I needed.  When he rang them up he tells me "shaZam! duuude, those are $9 a piece, sorry about that.  I left with three and it turns out I needed 2 of the 2.55's so I get to go back tomorrow and make the exchange, and maybe even trade in my old ones for half off the cost of the ones I bought.  If they don't take them I'll ship em to whoever needs them.

I've got my new main jets but still waiting for the pilots 

well, theres your problem  zeron clreance

Update: New pilots showed up at the dealer the day after I picked up the mains I ordered.  I've got them in my carbs now so now I'm at

125 Main
40 Pilot
Needles with a single #4 washer in addition to stock spacers

Still waiting on part number 17 from the carb fiche on bikebandit. Its that little o-ring that goes on the float assembly.  I dont KNOW that anything is wrong, but I trust em and  I'd feel better if I replced them when I had the chance. I think I'm gonna put the bike back together and see how it runs with the old o-rings. If its running alright then I'll put those on some other time.

My $2.99 carb balancer is made and the fancy $20 walmart compression tester is standing by. I figure I'll balance the carbs and see what happens.  If the carbs balance and my problem is solved I'll return the compression tester to save the cash and just ride until it gets too cold out.

Still need to figure out where I'm gonna mount the fuel filter. Its one of those little glass and metal ones.  I don't have a frame petcock (putting one on this winter), the lines just drop from the tank straight to my carbs so any suggestions as to how/where to mount this thing would be appreciated. Would letting it rest against the crankcase be too much heat? Should I plug it in closer to the tank?

Did you get your valves all sorted out? If so, I bet once you get your carbs back together and ballanced, it should work just fine. 

You can put your filter anywhere between your carb and the tank. Being glass and metal, I don't think you need to wory about heat  the rubber fuel lines would melt and the gas burst to flames long before the glass and metal would melt. You only need to wory about something hitting it and breaking it. Just stick it in the line and make sure nothing will hit it, or tie it off to something to protect it.

For $20 the compression tester would be nice to keep. Whenever you clean your plugs, you can check the compression, that way you can see if your rings or valves are starting to go. You get a warning when you need to do a rebuild long before your bike dies, so you don't get stranded.

You should figure out how much those jets will be to send them my way. I'd like to get that last little bit of my carbs sorted out too 
Thanks and good luck 

Check your email regarding the jets. I'll send them via usps priority or something, you should have them next week

Cool 

I have a plastic fuel filter sitting on my engine case with no problems. 

Alright, with the new jets,  clean, happy carbs, and dialed in valve clearances the bike seems to run much better.  Its not all together yet - still working out the gas tank issue (my other recent post).

The carb balance worked great, best $2 I ever spent.

Once I get the tank cleaned I'll be able to ride and see if all this was really worth it.

You'll have the thing running great just in time for the snow  oh well. At least it'll be running. Did you check your compression or are you still planning on taking it back? It should run just fine either way.
good luck