>>>*One cause that matches your description is a weak EGR valve. By the time these engines get ready for a rebuild they often have many thousands of miles of service more than most other designs.

The rebuild should bring the engine back up to specs, then we often see the EGR valve popping open slightly at idle. This can be enough to cause a mild skip or misfire. Since unhooking the TPS seems to stop it, that makes me suspicious of the EGR.

You don't mention if any engine mods were done at rebuild, this can also contribute. Certain types of headers, like the 4 into ones can give a sense and sound of missing when they actually aren't.

A true misfire with show up on an exhaust analyzer instantly. If the emissions spec normal, she isn't missing.

On the timing setting, with modern equipment most dealerships have, they should know where the timing is best set. We are finding 6? baseline and sometimes even 7? as best with our own rebuilds, but not always.

The computer should set the actual timing at speed where it is best anyway, the idle setting is just a baseline beginning point.

One other place to check is the injector pattern, unless there is an electrical concern, skips, misfire, hesitations are typically fuel related. If off a tad, she will skip a beat now and then.. There are other possibles but your tech most likely would have caught the obvious ones.....*EB