What you did just eliminated the ignition system as the problem - so now it's a fuel problem
Air in the filter only indicates air in the filter - fuel flows right past the air bubble - I think you have a fuel pump problem - I just worked on a 500 that had the fuel pump full of dirt preventing it from pumping adequately
The fuel pump has 3 small 'breather holes in the back plate - the plate covers a diaphragm - the vehicle was ridden for 10 years before the air space behind the plate filled with enough dirt to prevent the spring that pushes the fuel drawn in by vacuum from compressing and extending sufficiently to push enough fuel to the carb at anything above idle.
The first pic shows the amount of dirt in the pump air chamber - in the second pic (if you look very closely) there is one vent hole behind the spring loaded pressure pad and two more holes at the lowest point of the part - two of the holes are almost completely clogged and the one behind the pressure pad is almost invisible from the dirt covering it. If this pump did not also have a pinhole in the diaphragm, it may have been cleaned and put back in service and it would work with the pinhole, but the pinhole allowed it to get a small amount of fuel into the vacuum line causing it to run rich all the time.
Your fuel pump may just need cleaned, but it's faster and about the same cost just to put a new Quantum pump on