Right, bit of a delay in getting some updates posted.
The swap went quite well actually, got everything in and lined up and it all fitted.
Regarding the vibration, I set the diffs up so that at ride height the pinions were parallel between the diffs and the transfer case, + 3 degs. As from what I read, 3 degrees is the tolerable difference that a uni joint can cope with. The RR tail shaft has the uni's running out of phase, so I slid the spline apart and lined them up. Also, the RR diff pinions also point up towards the transfer case. I believe the "out of phase" uni's mated to the pinion angles being so far off parallel would cause a lot of vibration when the tail shaft is on an angle with the Patrol diff.
Uni's need to work, and if they are "in phase" and parallel, it doesn't matter that they are on an angle, whether up and down or across the car, the uni doesn't know which direction the tail shaft is pointing, as long as the pinions are within 3 degrees and the uni's are in phase with each other.
Anyway, this is how I set them up and the car does not vibrate. There is a grumble on deceleration, but that has been there ever since I have owned the car and I think I have found it in the way of a broken engine mount.
I have taken the car out twice and at all speeds up to 110km/h, I have not had any noticeable vibration. Out on the tracks it has performed really well, until Sunday. I hit a particularly nasty hill climb, bounced off a rock and snapped a trailing arm and spat the coil out. My own fault though as I was hard on the loud pedal. The damage list was a snapped LHR trailing arm, a bent RHR trailing arm, a snapped drive shaft and both engine mounts and one trans mount. Although one engine mount I had suspected was already broken. A couple of ratchet straps to hold the diff in place and we towed it the ~30kms home.
None of my fabrication or modifications had failed.
With the brakes, all I did was blank one front caliper line on each side, one out of the master cylinder and one off the proportioning valve. Brake pedal is high and hard and it pulls up pretty good. For the record, it's 4 wheel disc. There is a slight vibration under high speed braking, that will be a front rotor.
