When riding around 50 or so my bike has an occasional sputter or cough. I can accelerate fine, and doesn't pop when decelerating. I've cleaned out the tank, new gas, new fuel filter, plugs,also new seal from the carburetor to the manifold. The bike is an 88 FXR, and it has the updated CVH carb. Any thoughts

 

Maybe when you cleaned out the tank and filter,
Some dirt got sucked up into the jets. Make sure plug
Wires are snapped on tight.

 

I disconnected the fuel line before I did that, so I don't think that's it. It's weird has power runs and idles fine. Just when cruising at a consistent sped of 50 or so is when it does it. Maybe a clogged jet?

 

If the bike has been sitting at all I'd say pull the carb and clean it. You've got a jet stuck.

 

or is it correct english to say "a stuck jet?",,,lol.

 

Check for loose electrical connections on your ignition coil. An intermittent problem like that can send you around in circles!

 

I took the carb apart and it looked pretty good. I made sure the jets are clear. Also did the spray test on on the usual spots, and no issues. So I'll ride here in a bit and check back in. I did notice that when I rev the motor, the head light dims a bit when the motor decelerates. So could an old bad battery contribute to this?

 

The headlight should dim when you decelerate...or rather, look at it the other way around....it should get brighter when you rev it as the charging increases.

The symptoms you describe can be caused by the accelerator pump "loading up" and the cure is to check to see if the pump piston protrudes into the pump body when at rest, if it does just file the end until it sits flush in the body.

On the other hand it could be many things, including having a thunderjet kit with plastic slide fitted.

 

Well it rode fine, but still did it. When accelerating to around 3k rpm, is when it does it. Then it seems ok while holding it there. Strange

 

3k rpm is about where the carb crosses over from low speed to high speed jets. Sounds like someone messed with the needle in the high speed jet or as Spanner said the slide.