Seems like the problem is fixed. It seems it was a combination of a few things.
1. The stock front shaft that was in the rear was not true
2. The SYE (not supplied or installed by us) was not installed completely correctly
First we ordered and swapped in a new rear driveshaft that was true and we trusted was balanced correctly. This was okay'd with customer as he was just going to swap the rebuilt shaft into the front to replace his stock one. The shaft was straight enough for that but he was going to have it checked/straightened. That caused the vibration to change when installed. It got better but was still not right. We found that when the SYE was originally installed (again, not by us) the output yoke was not tightened properly. We tore down the NP231/SYE to get a baseline since we did not do the install and I have seen mainshafts that were bent from this particular manufacturer. Once we confirmed that the output shaft was straight we reassembled the 231 (fixing another issue with the SYE install that we found while taking it apart) with a replacement output yoke. Took the Jeep for a test drive and the vibration was gone. Looks like the fact that the yoke had been a little loose had worn the splines enough to cause an issue at speed. I did put a dial indicator on the seal surface of the old yoke, before tearing into the 231, rotated it, and it spun true by hand. At speed however, that was a different story.
Just wanted to follow up so maybe this will help someone else out there if they have issues.