I upgraded the main jet two years ago with the kit from Lancer.  It has run fine up until this point.  Maybe I should take another look at the filter however.  Not something that I have changed on a regular basis.  Maybe check the TEV also?

First of all, no part of an air filter is going to affect idling or low speed running in any way..shape or form,......neither is main or midrange jetting.

Symtoms you're having could be anything from valve adjustment, valve timing, (cam chain) ignition timing, or a very lean fuel problem.
If I had to guess which, I shouldn't, but I guess I'd call it out to be a carb problem.

What happens when you choke it while opening the throttle,......does that help or hinder ? Then take it from there.

take the air filter off as a test and she how she runs.

The only thing I can come up with at this point is that there may have been a small amount of old gas left in the tank that mixed with the new gas.  Or maybe the new gas wasn't good.  I'll replace the gas this weekend and see what happens.  I also rode her around a bit yesterday to see if running her around would help.  I noticed that with the choke all the way in, she would die very quickly.  As I moved the choke further out I could give her more throttle before she bogged down.

I hate to thread crap, but I think I'm having the same problem with my roommate's bike. When he first bought it, it had been sitting for a while and ran, but not well, so we cleaned the carb. Shortly after that, it started running worse -- dying when slowing down for lights, backfire, sputtering, flames, etc. I accidentally killed the battery one night, and when I charged it back up I couldn't get it running for more than a few seconds again. Now I can't even get it to start (though it is certainly trying to), but it slowly leaks fuel into the airbox and onto the ground. It emptied its own full tank just sitting in the driveway for a week or two.
I had my roommate order a DynoJet kit thinking it's a clogged/broken jet or maybe we messed something up when cleaning the carb. It sounds from this thread like I'm on the right track. Am I? Should I also get him to replace the carb boots and the vac line? If so, where's the best/cheapest place to get them? I'm going to make him buy a fuel filter, as well - what kind should he get/where should he buy it? (I'm guessing just a cheapo from autozone will do.)
Somewhat offtopic: the bike has a Supertrapp pipe, but no actual disc-muffler thing on the end of it. I'm guessing, then, that it's just acting like a straight pipe? Is that okay for the bike?

I still haven't got her running right although I'm at a point where I won't be able to work on it for awhile.  My back has been getting worse over the past couple of weeks.  Im scheduled for back surgery on Monday so it will be some time before I recover and get back to it.

dehydratedH2O wrote on 03/28/12 at 22:06:39:
You need to check your petcock, should stop the flow when off.  check the vac line for fuel, shouldn't be any fuel.  And you need to replace the float valve.

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There's one there I like, kinda big, but ends at a right angle so feeds right into the carb.
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A supertrapp with no disks will give you lots of tuning problems besides johnny law coming down on you.  It'll run very lean.  So unless you put in a big disk... you need to figure out some way of closing it off a little.  I think I would screw a plate on the back to close it off completely and drill a pattern of 6, 1/4" holes initially.  And you can make them larger to suit.