I have a 96 FLHR, just had the carbs rebuilt, and all of the upperend gaskets replaced. The bike has had a hesitation/sputtering ever since. At first it was lower gears and take off. But now it is at cruising speed. I can take off fine and go thru the gears NO hesitation or sputtering, but at cruising speed or when going up an incline and trying to maintain speed, it acks like its starving for fuel. Back off of it or drop a gear and slam the gas and works fine until you back out of it and try to cruise again, then the same crap happens. I'm lost...

 

My first thought is an air leak. Spray WD-40 or something that wont hurt the paint on yer engine at the intake clamps while at a high idle warm engine and cold engine. And at the seal where the carb mounts to the intake. If the rpm's change at all, you know what to do... Pay attention not to let the spray get into your carb throat as it'll give ya a false indication.
Other than that, I would make sure you dont have any loose jets inside the bowl and make sure the accelerator pump is working properly. Last, check the float adjustment.
I cant think of anyting else. Start with the easiest to do.
jim

 

Defintley sounds like you rolled a intake oring

 

If you do the intake leak test first-great idea to start there-and you have no leaks, then you might want to post the jets your rebuilder used in main and slow speed. Probably, NOT problem in main her and not accelerator pump. You can easily see that pump working to verify. Try going down the road with the spring and the use the choke/enrichener and see if that helps. You just may need a larger jet. Any other mods done?