My first thought was u joints with the vibration, but after having the driveshaft professionally rebuilt with new u joints and all and seeing no real lasting improvement, I am convinced most of the dl vibration after lifting is due to the new different angle of the pinion in the 3rd member side.
As far as down travel goes I am the same with ldub with the ball joint flip and ultra low bumps on the front, so i do have some down travel left at rest, but you would be surprised to note that the first thing to make contact now is the bolts that connect the front cross member to the frame.