The shop called yesterday and they had opened up the rear diff. The bearings were damaged but the limited slip and the ring and pinion were fine. He was pretty adamant that synthetic oil should not be used in this type of diff. Limited slip additive is not needed but probably won't hurt. He thought the grinding/shuddering sound I had may have been from the limited slip and using the wrong oil.
I was torn about reusing the AAM ls but decided to have him put the AAM ls back in (extra grand for the tru trac) They cleaned it up, put an new bearing kit and 85/140 oil. They even painted the rear axle and diff cover w/ what appears to be undercoating?. Looks good and runs great. They want me to come back in 2500-5,000 miles so they can remove the cover, inspect everything and change the oil.
The real test will be to hook the trailer up and put some loaded weight on it to recreate the earlier scenario. Need to wait a bit for that.
Nice shop to work with.