Why not upgrade all that you can when the engine is apart for repairs? We figured our Jeep could benefit from slightly improved induction, so here's an upgrade that might be hard to quantify the impact of, but it is clear either way that the new manifold has much better port geometry than the old. The new part is Mopar P/N: 05281803AA and comes from the newer 3.6 found in the JT/JL and others.
Stock JK on the left, PUG on the right:
The install is very straightforward as it fits just as the original did. The only modification I made to the manifold was to sand down some of the sharp plastic left behind from manufacturing as this can't be good for flow. We did also upgrade the oil filter housing and fuel injectors while it was all apart.
All in, this wasn't a very difficult or expensive job. We'll update further once the Jeep is back up and running.