I had unbted the trNsmission and allowed the drivetrain to angle down a bit so I could slip the axle out on one side and when I bolted it back up I found that the engine shifted back a tiny bit. The only problem now is that my rain hats on the PMOs won't fit. It was a close fit before, but now it's too tight. There isnt much slop in the engine mount, but I need to loosen The bolts and make it slide foward a quarter inch or so

I'd loosen the tranny mounts as well.

Also check for broken mounts if it's a late 4 cyl.

IIRC you have a 6 cyl conv with a RJ engine mount?
If so the engine mounts are bolted into a slotted grove (front to rear).
This may have shifted towards the rear causing your problem.
Worth a look at it to be sure.