through my experience, and if I understand this correctly, the problem is applying the torque. weather its a slipping clutch due to grease, or a flexing drive train, it comes down to torque moving members and a non-linear application of power.
I have 33's,3.50 gears, 2" body lift, stock rear spring pack, brand new body-transmission-motor mounts, and had clutch chatter/body shake while letting out the clutch into 2nd and 3rd gear of my np435.
it turned out to be rusty kick panels. After patching my kick panels, which reinforced the body to the frame, and eliminated the movement between the two, I now have a "linear" relation between the body and clutch. Chatter gone.
What do your kick panels look like? it sounds like you have covered most everything else.
mine were rusted where the front door post was, all the way up to the top of the dash
-slow