One other thing to check: shaft end play. I noticed this when I was building my stocker yesterday. If the main bearings arent' quite seated when you put the shaft thru, it is possible to tighten down the retaining collar and think you have removed all end play in the shaft, then when the bearings seat properly the shaft will have some play. This will of course move the relative positions of the head and the swash, resulting in collective pitch changes as the shaft slides up and down thru the end play.
Even as little as 0.040 inch (1 mm) end play can make a huge difference in pitch at the blades.
Properly adjusted the end play should be 0.0000 to 0.0005 (yes, half-a-thousandth of an inch.) So this means tight but not too tight, just enough end play that you cannot see it but might be able to feel it if you are sensitive.