Hi Matt,
It is a very strange problem you have there, but great report on your problem and your efforts to resolve it. Its good to have all the information on what you have tried so far.
Usually with something like this it says to me there is something amiss in the head somewhere, have you tried another set of blades by any chance?
Also, do you grease your head dampers? If not i recommend this as it allows the head axle to float much easier as an ungreased axle can produce an effect like your experiencing. I use a silicone rubber friendly grease (Tri-Flow with teflon), and use a very small amount on the dampers and axle surface to help it to float.
Do the blade grips rotate freely when they have no blades or pitch control links attached to them?
Have you checked the head axle for true running?
Have you checked the main frame assembly for squareness?
Couple of things i would try, and although you have done some of them before it's worth double checking:
1) Check Main shaft for true running
2) Check Head Axle for true running
3) Completely dismatnle the head assembly and check the entire assembly, make sure everything is in it's correct orientation etc.. Thrust bearings largeID to inside, smallID to outside etc.. make sure there is no extra shims in there etc..
4) Grease the head axle if you don't already
5) Check the frames for Squareness
6) Change the main shaft & head axle
When you change the main shaft loosen the lower bearing block and allow it to float in the frame while you install the mainshaft in the two upper bearing blocks.
Hope this helps and let us know how you go.
Cheers,
Ross