Im in the middle of a frame off and I am bolting up the tranny and skid plate, but ran into a problem. With the skid plate on the tranny it is an inch an a half too far to the driver side, which makes me think that I put the motor mounts in wrong... There is a metal tab on the rubber mount is that supposed to be facing up or towards the ground?
When I swapped trannies and skid plates, I thought I was about an inch and a half off also, turns out I had the skid plate mounted on the wrong holes and the hole that was off 1-1/2" wasn't even the right hole. When I finally mounted the skid plate in the correct holes, the tranny dropped right in place.
The mounts on the engine itself look almost like FSJ (wagoneer) mounts. That might change the position of the motor (I know it makes it sit high).
If I remember correctly, the transmission is offset to the drivers side just a bit due to the transfer case. Use a level on the inside of the frame in the back, and measure over to the rear axle yolk to see if the yolk is centered or offset an inch or so. Make sure the output of the transfer case is on the same plain so you don't have a compound angle with the drive shaft.
Beat it to fit, paint it to match!