I would replace the fuel filter, check the flow coming out of the fuel pump
and check your air filter. You might have a mouse living in your air intake box - engine needs fuel and air to run.
If the air filter is not white like paper replace it. You will be surprised how badly these little air filters will choke off the engine when they are dirty.
If you dont want to pull the carbs apart again, run a pint of Seafoam thru the bike 4 ounces per full tank of gas. As long as the engine will run at all, the seafoam will flow thru the carbs and wash gunk and goo out.
Also have to ask the obvious question: is there old brown gas still in the gas tank? If the gas is not clear drain it out. If you dont know how to get rid of old gas, just put it in an oil drain pan outside somewhere about a gallon at a time, and it will evaporate in a few days.
there is one other possible cause: the bike has a throttle position sensor (TPS) that tells the ECU how much to advance the spark. If its not connected or not giving the right position signal, the ignition timing will be off - it might idle ok then die under load, or the other way around, depending on what the sensor is telling the ECU. Something to check. Its a simple resistive potentiometer on the butterfly shaft on the carb, you can check it with a volt meter.
If you dont have the factory service manual for the 650, you can google it online - free in pdf format. That will tell you how to check the TPS.
Last edited by KCW; 11-14-2018 at 10:09 AM.