IF the dealer wants to run the bike on the dyno instead of on the highway to try to track down noise problems, assuming they have the proper kind of dyno with a load cell and not just a straight inertia type dyno, that could be a valid method to verify and diagnose the issue. Kind of hard to ride down the road and also check for noises with your handy dandy stethoscope at the same time. On the other hand, if all they plan to do is a wide open throttle max power run, that won't do anything to help solve your problem.
Here's the part that I don't understand. If the bike was OK before they replaced the cylinder, and it wasn't OK immediately after they replaced the cylinder, why are they having a hard time figuring this out? Sounds like they either got some bad parts (Harley shipped a bunch of tapered cylinders, for instance) that they didn't check before they threw them in, or they screwed something up during the disassembly/assembly process.
What the other folks said about calling H-D direct is right on the money. Do not sit back and let the dealer jerk you around until your warranty expires. Get everything documented (hopefully you kept copies of all previous repair orders) and get it on record with H-D. Explain what has been done, what your current problems are, and ask them to get those issues resolved for you. The warranty is from H-D, and the dealer is just the agent. H-D is still legally responsible for the warranty.
Good luck.
Jerry