Thanks for the replies.
I did find an intake hose routing schematic on line. The only problem was that the vent hose connecting to the float bowl vents and then running into the series of connections * going nowhere * and also to the top of the air box was plugged. There is a 'T' that should be left open as a vent I guess and it was capped.
The other change I made was to bypass the carb float bowl coolant network. I also checked the fuel filter and the petcock screens, both of which were fine.
It's hard to tell without pulling the plugs to tell if this problem was an over rich condition or a lean condition. Since it started running better with full choke, my guess is somehow it began starving for fuel for whatever reason.
The bike runs so much stronger now. I took it out for a couple hours, and while it was a cooler day, I think it's going to be ok.
I almost forgot, it seems there was originally a heat shield down there between the engine block and the carbs or fuel line? I made a temporary make shift insulator from fiberglass insulation wrapped in foil. That may have been a problem too.
Again, thanks guys for your input and ideas!