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The only places I would think to look for air leaks would be the 2 boots between air box and carbs, the carbs themselves, and the 2 boots between the carbs and the engine.  Are there any more places to look?

Start with those places and go from there!

Another common source of air leaks (especially considering you have taken the carbs apart) is to have misplaced the tiny o-rings that fit into the top of the carbs. A search should turn up lots of threads with pictures, diagrams, fiches, etc. Ask if you don't find the right info.

I found a leak at the bottom of the left boot between the carbs and the air box, no leaks at all from the carbs or, more specifically, the vacuum caps.  I then replaced the hose clamps with something that could get tighter.  No more leak, but no noticeable change in the engine's behavior.  The bike still dies without the choke and hesitates under 4500 RPMs, even after confirming that I sprayed carb cleaner and inserted a wire into the "slow system" hole.

What else could cause the bike to die without the choke.  I'm now a little fixated on the pilot jet... How can I confirm that I did check this out?  Any pictures or description of where it sits?  When I disassembled the carbs the first time, following the FAQ directions from this site, I was supposed to tap a hammer on the main jet (http://gstwin.com/carb_work.htm) I couldn't knock anything loose so I just soaked the hell out of it.... is the pilot jet what I was supposed to dislodge for cleaning?   Time to take the carbs off again?   

Thanks again.

Pilots once you remove it, usually should not be reused. They are likely to get damaged and if they do, getting it out will be a beeyatch ...
Anyway, I can rejet and trouble shoot, or sell you a jet pack for a stock bike with the right pilots in it. Usually you can make the same mistake over and over and wonder why the problem keeps comming back ...
Cool.
Buddha.

What do the sparkplugs look like?

Here's a thread with lots of details about the missing o-rings; the symptoms sound very similar to yours (you may want to take the carbs off again and recheck):
http://gstwins.com/gsboard/index.php?topic=40662.0

Image 7.8 (B) shows the pilot jet location:


I can't imagine that you missed it?    However, if the pilot jet is clogged, it could cause the problems you are having. Again, I would suggest looking at the carb insides another time... sorry 

Keep trying, you'll get it!

SUCCESS!

I pulled the carbs again and after confirming what the pilot jets were and that I had removed / cleaned them before.  I pulled them out again.  Both came out without any issues and with no damage to either.  I flipped one over... no jet hole.  Then I turned the other one over... no jet hole.  Both had become completely impacted with gunk.  This must have happened in the last 3 weeks.  Anyway, I soaked and cleaned them and the tube internal to the floats, inspected everything else, and put the carbs back together again. 

Next I thoroughly inspected the carb-engine boots, no issues.  Then I installed the carbs and thoroughly inspected the carb-air box boots.  My best guess is that over time the carb - air box boots warped, so this is why the old hose clamps were not effective.  I then very carefully installed the air box.

Start the thing up and.... perfect.  I think it must have been about 3 small things and 2 big things (clogged bypass ports and pilot jet) together.  Now the bike idles fine, starts fine, runs fine, if anything now the bike's throttle seems a little touchy -- maybe because I haven't ridden in a while...  The only thing of note was one stop sign, the bike stalled when I went to accelerate.... it only happened once and after the last few weeks, I'm willing to write it off.

Thank you to everyone for their help, especially beRto.



Now, I guess I'm off to the front fork main seals and chain... 

 

Fantastic! Another GStwin success story 

(sorry Buddha  )