18-04-16, 10:51 PM
Welcome.
Presumably 2&3 chime in once the revs get up a bit, I can't believe you'd ride 1000+ miles on two cylinders!
Combustion problems are either mixture, compression or sparks.
Examining the spark plug tips can give you a fair bit of info about the mixture and checking the spark is easy enough, just bear in mind that the cam cover is insulated so get the spark to jump to a cam cover bolt or some other part that's connected to ground.
Make sure the carbs are balanced and the throttle position sensor is set correctly.
There's a good chance that there are some blocked jets or problems with the float valve. Drain the carbs and catch what comes out.. water or grimy/rusty petrol would indicate that a good clean is needed.
Check the fuel level in each float bowl using the clear plastic tube on the drain method.. details in the downloadable manual.
Let us know how you get on.