If you have both a #110 mainjet and an EMGO air filter, you've found the troubles. Go to a #105 mainjet and try it with simply no air filter in the box.
Like David 750F said, the total air inlet size needs to be no more than 1.25 X (the cross-section of one venturi of one carb). In the airboxes like you have, with the 'quieting' vent on the bottom facing backward, this particular one can benefit from adding 2 holes of 1/2" size thru the floor of the box and NOT thru the vent to the outside. This reduces the tumbling of the air at higher velocities (bike speed down the road) inside the box by breaking up an effect we used to call "drumming". The only way I know to describe this that others may have experienced is: at 50-60 MPH in a 4-door sedan, with only one rear window rolled about halfway down, the interior air of the cabin will alternately drop-rise-drop-rise when at the right speed, causing a drumming sensation in our ears. This, in this particular airbox, was demonstrated by a rider who 'straight-raced' on a flat, straight road in New Mexico on a 1977 K7 model with a cloth streamer hanging out of the airbox (on purpose): it alternately flapped out and back in, as observed by his buddy on a Harley next to him, circa 1980. He was the guy (that I know of) who drilled first 1, then 2, then 3 (which he later plugged, back to 2) 1/2" holes in the upper floor of the bottom vent. The bike picked up almost 10 MPH top speed for it, outrunning his buddy in the end.
This 'drumming' effect (my term, not his) was likely not even considered by Honda in 1977, as the major customer (USA) was sporting a blazing 55 MPH speed limit at the time. Honda was under the DOT's thumb then to make the bikes quieter in a full-throttle, 2nd gear pass to a microphone, recording the sound levels and being required to keep it below 78 dB. And, ONLY Honda was forced to do this as "the example to all importers", because Carter was pissed off at them...