I think I've probably got a clogged pilot jet in my bike because its only been run a handful of times since may, but Im not sure.

The idle was low and a little "thumpy" when I first picked the bike up but it didnt stall out after closing the throttle.  I started to have problems as I got stuck in traffic on the drive.   I had to flutter the throttle and keep the RPMs high enough at idle to prevent stalling (still happened a few times anyways, using the front bike and keeping the throttle open enough in stop and go is tough)  I finally got enough time to reaquiant myself with the idle screw, but I still had problems with it stalling at closed throttle.  After stalling I would start it back up and it would idle smooth and fast until I got to the next stop, where it would repeat.  

Im sure its not the vaccuum, because that's already broken and I was using PRI.

Am I right with the guess that my pilot is clogged?

both ends of the vac line are plugged off?...
Then I would check the air filter, spark plug, make sure the idle speed is high enough, if it ain't any of those, start cleaning the carb jets and passageways.  Good luck,

what does the spark plug look like??sounds wet to me...

Running on prime w/ the vac line capped at both ends will by-pass the petc0ck vac,
but if you run o.k. on reserve, it operates on vac just like the main, so that means the petc0ck gas screen in the gas tank is blocked up, or the ball behind the petc0ck selector knob is plugged.  Not a likely thing, as you will usually see it plug up the reserve area and not the main, due to lack of use, unless the PO always ran it on reserve.
You might want to just pull it, take it apart, and see whats going on in there.  Not to bad a job, just make sure to drain the gas tank first...
Hope that's not too confusing...

Here's a link to the parts fiche, if that's any help.
http://fiche.ronayers.com/Index.cfm/Module/Main/TypeID/26/Type/Motorcycle/Mak...