If you are at high altitude you might be running too rich.

^^ this ^^ it is about 5000ft is it not up on the plains?

I posted in another thread of yours but it sounds like your running really rich.

A lot of people seem to rip the front of the airbox off (which kills a properly jetted motor) as a cheap compromise to lean it out a little.

My advice would be to get the airbox back to standard and get to a dyno operator who can get the fuelling sorted out, then it will run spot on.

with the airbox missing it wont run right when jetted to suit the environment.

You did check tank breather didnt you. when you have problem and stop is there a sucking noise when you release the fuel filler cap. I had a problem that sounds just like yours from a blocked tank breather.
all the best.