I want to take a minute to close this thread since I found the problem:

Turns out the 2.5" x 2.5" steel that I uses to build the body jig was not very rigid. Even though I leveled the jig, the weight of the body parts caused it to sag in the areas without a jack stand directly underneath. This was maddening and I felt like I was chasing a ghost. The jig was square the entire time. . .

If you're building a body jig, ensure your using rigid steel!

For those who have provided guidance, THANK YOU!! Pictures of the build coming soon. Building from the ground up with all brand new parts. What a b*tch!!