Just curious, but where is the fuel tank located? In my COE, it is behind the seat. Sitting at this height it is easily high enough that the fuel pump really isn't needed.
Add an inline fuel filter directly under the tank, before the fuel pump. If you have any crap in the tank it will continue to be a problem with clogging the carbs passages.
I had dealt with a similar instance with my truck, it would run, but pretty much any time it was turned off, crap would settle and plug the carbs passages.
As above stated, check your timing, adjust your valves and with an inline fuel filter, you should be set.
Jeff