Lookin' good. Did you change your slow jets? I went from the stock 38s to 40s when I installed pods on my '75 CB550K, am still fiddling with the air screw settings; currently set at 1.5 turns. Did you adjust the float height?
Your misfiring cylinder reminds me of a problem I encounter fairly regularly. The float valves seem to want to stick in my carbs ('77 PD46A carbs on my '75 motor; who knows how they got there). I have installed new float valves, polished the seats . . . they still stick. This causes the bowl to overflow, and no fuel gets through to the cylinder. Sometimes this is intermittent, as in one cylinder "misfiring", failing to run, as you are experiencing. Sitting at idle seems to bring it on, as does leaving the bike on the side stand rather than the center stand. The roadside remedy for this is to pull over someplace where you can set the bike on its center stand, and determine which cylinder/carb is not firing (touch the headers CAREFULLY, and watch your overflow lines for leaking fuel). Close the petcock and drain that carb's bowl (mind the gas fumes; do this in the open air), close the drain and reopen the petcock, then watch the overflow tube. If it pees gas, you're still stuck. If it doesn't pee, start 'er up and see if you have gotten your cylinder back.
At first I thought this might be related to possible sagging of the carbs -- with no airbox in place, they are supported by the rubber intakes and the cables only. I make a carb support out of a couple of long zip ties, looped through the upper rear carb brackets, then over the frame. You might consider trying this, if only to take the strain off your rubber intake boots.
Will be following your build -- good luck!
