Heavy shafts of 1.5" or more will naturally compress the rubber bearing on the bottom side, but not so much that there's an obvious gap at the top. Photo #1 illustrates a clearly misaligned shaft. Next, check the shaft-to-bearing alignment at both the front and back ends of the bearing.

One other thing to look at is when the truck is in idle and in park look underneath and see if you can see the motor moving. That is another way I chased it down. Engine was moving but just barely and then by the time I got the the Transfer Case you could really see it. Just to help.

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how to check engine mounts