Novak Conversions Jeep Wrangler TJ engine mounts

Rear axle alignment

That possibility is not one I would be willing to just assume is the case. I'd still be checking the engine mounts, that's a lot of movement at the tcase for a rubber motor mount bushing.
The stock motor mounts are very squishy. We shove the trans back and forth several inches when we build stand alone cross members for custom belly skids. They are a fair bit forward of the trans mount and not that far apart so it only takes a small bit of movement at the motor mounts when the trans mount upper moves 2-3". In fact, they are so easy to deflect, we measure the center of the output shaft on the t-case over to the frame on both sides and keep that as a reference due to just how easily you can off center the output with a floor jack. All that has to happen is a few grains of sand to stop the jack wheels from rolling with the load and the drivetrain moves to the side.

When we clearance the tub for a raised belly skid by jacking up the t-case and putting a socket on top of the case corner where it contacts the tub, we have to put a ratchet strap around the tail shaft to stop the drivetrain from shifting over since the trans tunnel right there is at a slope which forces the case over.
 
Novak Conversions Jeep Wrangler TJ engine mounts