Diagnosis needed
 

On the way into work this morning my bike temporarily dropped firing on one cylinder. I was going through my usual routine...down to the corner gas station, fill with gas and get on the road. The only thing that was different today was a really filled the tank to the top to try and get exact change.

So I get on the road and about 3/4 of a mile out the bike starts to sputter and goes WAY down on power. I was in the far left lane and it took me about a mile to get to the shoulder in heavy morning traffic.

Pulled off and shut the bike down. The only thing I could think to do at the time was pop open the gas cap to possibly relieve pressure if the vent line was clogged. Just guessing here...

When I fired the bike back up, it fired on one cylinder for about 5 seconds and then the second cylinder kicked in and it was running normal as ever. Rode the rest of the way to work (33 miles) without incident. Cruised for most of the way and then opened it up towards the end to "clean it out."

Anyone have any ideas of what might have happened?

Could be that one of the coils or spark plug connectors was loose.

moisture in the bottom of the float bowl on the carb of the cylinder that wasn't firing

These two things are the answer..... you overfilled the tank which caused the vent line to become blocked.

When you opened the tank you released the vacuum lock which then allowed the float bowl to refill and the bike to run normally again.

^^ What he said. This has happened to me twice. Yes, I didn't learn the first time.