One area where I have previously had odd main rotor vibrations (500D) that come and go was worn main rotor pitch change/flapping bearings and pins. These are the bearings (spherical) that are bolted to the pitch change cases 5 off (excuse terminology long time since I touched a 500) and the pins 5 off attached to the hub by nuts. A 500C would obviously have 4 of each.
To check remove blade and try to lift the pitch case keeping it horizontal feeling for play.
They can give a rough ride while exhibiting a fairly good track.
The teflon inner lining of the bearings wears out and the metal to metal contact wears and steps the pins.
When looking at a visual tracking picture you see one or more blades moving up and down for no apparent reason.