My positive and negative cables were loose on the battery. Not so loose that you could see it but if you grab the cables they moved easily. Tightened them down good, fired her up and she ran fine.

Now for the but part. I am noticing that at the top end of each gear the bike seems to stutter or hesitate a little. When I change the gear it goes away until I reach the top end of the next gear. Does this through all 5 gears. I am not really redlining each gear out either. Just normal speeds.

 

To me it sounds like it could be a vacuum leak, the engine would run worse when cold and needs more fuel, or at upper rpm's when it is leanest. Try to spray some carb cleaner around the intake and see if the rpm's pick up. My Road King had the rubber plug on the intake leaking, it was cracked from age.

 

My road king is fuel injected. Would your suggestion still apply?

 

Is your air filter clean and un-restricted? I would look at the ignition system starting with the gap on the plugs, .038 to .042 is good. If it has been over a year since you put new plugs in, you might replace them. It also could be plug wires. At higher rpm your engine creates very little vacuum, but you could have an intake leak causing a lean condition.

 

Yeah, it's just used to find a vacuum leak, but don't be fooled if the intake sucks some in and the idle increases. Try to keep the spray to a minimum, just a shot here and there.

 

Replace the filter and check the pick up strainer. You will be surprised what you will find in the tank. And as mentioned above, pin hole in one of the lines.