When the engine is cool it runs OK. But when it gets hot you can feel a distinctive thump of the cylinders in your but and back. When sitting still it really gets on your nerves.You can feel it at all speeds and at faster speeds 70 to 80 its annoying and beginsto hurt your back.Just came back from the alabama hog rally. Not a very good ride on my 06Road king. Yes I have had it to 3 dealers and they say everything is within specs. This started at 2,700 mile and there is 6,000 on the bike. PCIII, Kerker slipons and KN air breather. This may sound funny but my exhaust note even changed. Any Ideas on what can be checked. I have given up on the dealers and have been told to find a good mechanic that can trouble shoot. Thanks

 

Get rid of the pcIII, sorry, just take it off the bike, buy a race tuner, and install the stage one map supplied with the program.
Then take the right side baffle out of the slip-on muffler and install it in the nearest trash can, order the Mikuni PAT baffle and go ride the bike, you'll like it.

 

Have you checked the motor mounts?