The carbs are very hard to get clean. Ultrasonic cleaning is probably the best. There are so many passages that just the normal cleaning with carb clean doesnt always work the first, second or even third times. Try spraying carb clean or little starting fluid see if the miss goes away.
The coils and wires go bad as well as the boots.
The number one problem that makes these bikes run terrible is the valve clearances being too tight leading to burnt valves and loss of compression. This is probably the #1 problem with these bikes, Nobody checks or adjusts valve clearances as they are a little bit of a pain. The honda spec is too tight to start with so valves start leaking fairly early in the bikes life.
start with seeing if it stops missing with some outside fuel...easy test to start with. Then a strong second is check compression...if its less than 120psi it wont run well if its 100 or below its not enough compression to run and you will have a miss
