Some more information is in order. How about the idle RPM checks, and your high and low RPM checks during the runup? When you do your runup on the ground, you should be cycling the propeller to see where the low RPM limit lies...should be about 1200, and you should be seeing at barometric pressure the same standard RPM you always see. Usually the high and low checks are done at barometric pressure, just shy of governing, rather than at a typical runup RPM of 1700 or so...in other word, the power setting for that check is set by manifold pressure, and hasn't pushed into a governing range.
The reason for doing it this way is because at a typical runup power setting, you're not exploring the full operating static RPM range for the propeller. By continuing to apply power to barometric (about thirty inches at sea level, about 25 inches at five thousand feet, etc), you're seeing the max RPM you're going to get static...taking he propeller as fast as it will go before the governor takes over and starts increasing blade angle or interfering with the propeller.
If the RPM is low at this point, you may have an engine that's producing inadequate power. Accompanying this you may or may not have roughness, depending on why the power loss is occuring. Generally a problem isolated to one or two cylinders will produce roughness and vibration.
If you're pulling manifold pressure in the order of 36", then clearly your engine is producing power, and it's being boosted properly. This isn't to say that it doesn't have problems, but if you're pushing the power above barometric, the problem with low RPM must be governng...something is holding the RPM down, and that can only be the propeller. The propeller is restricted by the governor, and the first thing to determine there is if the governor limits have been changed.
A low RPM could be a linkage issue, restricting the governor limit (working the same as the propeller control being retarded). It could be debris in the pilot valve, sludge in the propeller shaft, a physical restriction to the propeller limits, a counterbalance issue (check for loose or shifted counterbalances), a broken speeder spring, a leaking governor assembly, or possibly other problems. But the first step is to see where it's failng to govern properly. If you're seeing a low RPM during the barometric check, and the engine is at barometric pressure, you have a propeller which isn't reaching it's high RPM pitch stops for some reason or other.
I'd also be for checking the individual blades very carefully as part of the preflight, looking for leakage around the hub and blade shank/hub interface, and any play in the blades themselves. Look for one that's different, rather than both blades having play.
I had a five blade hartzel on a turbine installation this summer that turned out to have a problem...it had a very occasional vibration that came and went so infrequently, and lasted for so short a duration, I thought it was my imagination or perhaps an unusual turbulence. It was found during a preflight inspection, and as manifest as a very slight play in one blade. It was immediately grounded, removed and overhauled.
Let us know what you find.