To close this out... I just drove the TJ for the first time in 6 months. Picked it up just now from the shop. There were two issues, one being the distributor. I would have swapped that out again next since I have two others sitting in my garage, but the bigger issue I might not have figured out.
The harmonic balancer/damper was bad. The rubber between the two halves had degraded and the outer portion had spun. So even after swapping distributors, the shop couldn't get the timing correct. This is the one thing I don't get, because I thought you didn't set the timing? Either way, new harmonic balancer, front crank seal, and distributor and everything is running great again.
Which is interesting. The first shop said the crank was wobbling. It's too bad that first shop didn't inspect the balancer and determine the actual issue when they noticed movement in the harmonic balancer.
*edited
Side note, the intermittent misfires the computer kept seeing, I wonder if that was due to the imbalance with the harmonic balancer. And I wonder how many other issues that created.
Now to clean up the TJ, reassemble the interior, electronics, etc so I can list her for sale!