Misfire/one cylinder not running/Rough run

using this post for pictures to help diagnose what the hell is my bike's problem...

Trouble!

So after a 100mile ride, about mile #80 bike lost power and did 2 big backfires, but rode home ok the last 20. I take the bike out again a day later and the bike didn't feel right or like it did have a loss of power. So today I cleaned out the carbs from back to front and inside and out, also cleaned and scrubbed the coils and grounds. Bike now runs rough and the carbs are acting really funny... I guess im going back to basics to figure out what's wrong now...

new "rubber"

New Rubber! well both tires and tubes replaced
I went with shinko 712's with 100/90/18 in the front and 110/90/18 in the rear, they were the same size is what was on the bike when i bought it and research has shown that going 120/90/18 on the rear is almost too tight of a fit with some problems. But don't get me wrong other say its fine and make it work but i had to nudge the wheel past the drum break and i think if it was wider you would have to deflate the tire to get it on.

Also had a bit of problems, bike started to basically have "no guts" and with some help from the forums decided it was the carb diaphragms that needed to be replaced. Replaced the diaphrams and put the stock carb boots back on to the airbox, i still feel like it runs better with the pod filters though.