When the engine cuts out, is the dash still on and registering mph?
If so, it's a loose connection or a bad safety switch.
Check all harness plugs you can find.
For the kickstand switch, put a jumper wire in the plug up under the seat. Ride it and if that fixes it, you can permanently disable or clean/replace the switch.
FWIW, the switch almost always works when down, it's the up position that ruins the day.
You could try putting the bike on a stand, running it with the kickstand up, in gear and then wiggle the kickstand to try and repeat the fault.

 

So I got her up and running today mostly. Here's what happened

I realized that the bike had refused to start right after I replaced another one of the Vacuum caps that I had put on when I did the smog delete. There was a small one on the carb, but also a big one on the front of the air box (both of which would have been letting the bike suck SOME air in bypassing the actual filter ... glad I caught that before it sucked tons of dirt through my engine! :O ). In between days of being able to work on the bike, I put that little bit of info in combination with the fact that when it was acting up it seemed to want a different amount of choke than normal and that fuel was absolutely getting into the carb, and i definitely had spark, I realized that it might be starving for air rather than fuel or spark. The only other time I've had an air filter so bad it interfered with the motor running it was a lawn mower that acted up more on hotter days when everything was expanded and tighter and the motor couldn't pull air through the gaps as well. This was the same, motor warmed up, things got worse, then let it sit a little and it would run a little longer. I thought it was worth a shot, so I took off the foam, washed it, dried it, and threw it back on just to see what would happen ... whala, bike fired right up and ran like a champ. I ended up replacing the spark plug anyway since I had the tank off and because I had bought one thinking that maybe that was failing when it heated up as well, $4 of peace of mind.

Down side is that I don't know if I can just spray some unifoam oil on my current filter or if I need to get a replacement filter before really riding it. I don't know if the filter is the original or if it's an aftermarket, I just did the hot water and soap bath and rinse to test my air-filter theory. Now I need to sort that, finish putting it all back together, and put some real miles on her.

The other downside was the moment when I was putting things back together letting the bike idle along for about 20 minutes to make sure everything was good to go when one of my fuel lines snapped and literally poured gas all over my hot motor which then was literally BOILING on it's way down to the ground. That freaked me out but thankfully no fire and no damage besides having to replace that fuel line.

Thanks for all the input guys, sadly I put a lot more time and energy into a dirty filter than was required, but the timing with the spraying of the ignition switch, the low mileage, the otherwise great performance, and the rotting vacuum cap all threw me for a loop as far as considering the air filter. Never expected a filter to need cleaning/replacement inside 3000 miles, but that seems to have been the core issue, that combined with some bad vacuum caps, some weird timing with another repair really had me twisted up.