Front end out of square.

I have a long arm kit installed and I had to push my axle another inch forward. When I adjusted it I gave each sides Jonny joints a 1 inch turn each and when I checked my axle to see if both sides were even from center of front to center of rear the left side was a 1/4 inch off from the other side. I'm going to double check to make sure my steering is perfectly strait and that my measurements are correct but will that 1/4 inch difference be much.
The left side is 101 13/16 inches and the right side is 101 9/16

I would take both lower control arms out and double check that both are indeed the same length for starters. A 1/4 in seems like a lot to me and would make your jeep want to drift to that side down the road. Figure if one control arm is +1/8 on one side and -1/8 of actual set measurement on the other, That will give you a 1/4+ out of alignment.

Check to see if the centering pin on one of your rear leafs is bent or broken.

No need to remove arms, just use a tape measure from center of bolt to enter of bolt.

Lots of things to look for, broken center pins, wallowed out bolt holes, bent brackets, etc.

You should be measuring axle squareness/alignment from a fixed point on the Unibody, not from axle to axle.

Measure from the same transmission cross member bolt on each side of the frame.