I have a 2003 Sport TJ with an NP231 TC. I installed the SYE kit and a new rear shaft after rebuilding the TC and Rear End. What I am dealing with now is a low frequency vibration that starts around 50 mph. I read another post on this forum in which the poster postulated the theory that the vibration could be mitigated by changing the mass of the TC and Skid plate. So I bought a box of 1oz. wheel weights and have been applying them to the skid plate and the TC wherever I can. It is reducing the vibration but it has not completely gone away. I think the reason 03 Jeeps have the balancer is because of this issue.
The problem is that I cannot find a Harmonic Balancer for the TC. I think it would fix the problem. However, with the SYE kit installed adding one most likely means rebuilding the TC again. That is unless I can find one that is designed for the SYE kit installation.
You might want to add some density to your skit plate and TC housing is your not going to use the HB.