Okay so here's the latest..
As I mentioned, Monday last week, I pulled the carbs and gave them a good cleaning.
Once I had the idle set the bike ran great. I was very happy because I had planned on riding to Vegas that weekend. The following couple days I found and fixed a problem with a throttle cable. Didn't do any long/hard riding (just my commute to work, about 7 miles each way), but as far as I could tell she was running fine.
Thursday I changed the oil and replaced the oil filter. Unknowingly at the time I had overfilled the oil.
Friday I start having the same problems again on the way to out meeting place before heading out to Vegas. Bike ran fine above 5K RPMs. Considering it'd be freeway riding the whole trip, and I already had everything booked/paid for.. I continued with the trip.
Everything went as expected. As long as I kept the RPMs above 5K and below 7K (which is were she prefers to run anyway), it was fine. Other then being cold at the end the ride was quite nice until I actually got there and had to deal with traffic lights and such.
Along the way I discovered I had overfilled the oil. My parking lot at home is slanted so the bike is not level which adds some guess work to things like oil changes.
This would explain the oil in and around the carbs I mentioned earlier (although some of that may indeed have been from a WD-40 job
So I drained the oil down to Low on the sight glass. Dumped some generic carb "treatment" in the tank (couldn't find SeaFoam anywhere in Vegas). I might have been in my head but there seemed to be some improvement but the bike was still having the same problems. Sunday I road home and noticed I could get above 7K RPMs (I never had the chance to safely test the limit). I kept it around 80mph and got home fine. I then dumped half a can of SeaFoam in the tank.
I've since made one round trip to work and the problems are the same. Fortunately I bought a dry-cell battery (as recommended here) which has made starting the bike as easy as pressing the button, so stalling at lights isn't so nerve wracking when it happens.
Sorry this post is so long. I thought if I wrote it all out someone might pick up on a clue. I believe the oil change had something to do with it. This originally started after a day of maintenance, which included an oil change but also a bunch of other stuff which confused the situation (did too much stuff at once, big no no). I'm quite sure I had overfilled that time as well.
However, with the oil now at Low, and having traveled 300 miles I would have thought any oil left in the carbs would have worked it's way out by now.
Would oil in the carbs even be a problem to begin with? Perhaps it's something completely different that I'm missing..