I think you guys have covered all the bases, but would still like to offer two areas to look into:
1) Governor to AFCU matching: Pratt came out with a bulletin about 15 years ago (sorry, do not have the number) which specifies governor P/N that is tuned to the latest AFCUs and helps reduce oscillations on the -3D. You may have done this already.
2) M/R servo input lever friction: as Bell went to "D" seals (D shaped O rings to help reduce oil leaks) in lieu of O Rings in the hydraulic servos, this drove to input lever friction above the desired value. This value is very low, around 1.5 Lbs if I remember correctly. This causes overshoots as the AFCS system pushes the lever until it finally moves and then moves too much. This was especially apparent during coupled ILS approaches, in very still air. Going back to plain O rings has helped reduce the friction.
Hope this helps.
Fly Safe, Always
