I would think a rebuilt trans would come with a converter. They wouldn't want to use the old one and contaminate a fresh rebuild. From what you are describing it sound like it's an issue with ignition. Inspect the cap/rotor wires and verify you have spark to all the plugs. If they broke an 02 who knows what else they did.

Yes a converter came with the rebuilt transmission and they got another transmission from Jasper and took the converter from that transmission and replaced it again. Didn't fix the problem. The transmission shop also tried replacing the cap and rotor thinking they may have cracked the cap while doing the trans job. The wires have about 10K on them as do the spark plugs. Pulled the spark plugs, they were clean and looked really good. Compression test was 130 across the board. Fuel pressure 45psi. I'm thinking my next step is the balance, even though I don't see the the rubber has been compromised in any way that is usually a tell tale sign that it has been spun out of balance.

Check the crank position sensor. They are frequently victims of trans swaps..... and even if it's only slightly bent, can cause some rather interesting issues......

I would think if the crank sensor was the issue i would be having a misfire. It's not misfiring just a vibration. Truck runs good.

The vibration may BE a misfire.......

Working as a mechanic for the first 18 years of my work life, I can tell that it is not a misfire its a vibration.

Have it your way......

If this started RIGHT after the trans swap, drop the starter, pull the dust cover, and turn the engine by hand.... Make sure there are four bolts holding the torque converter in place, and that there is a weight or two on the converter somewhere.... May need a mirror, or something, to be able to see everything......

The 5.9 is external balance, and pre-96, the balance weights were on the converter, so, one bolt hole is offset from the others, to ensure the converter only bolts up one way. On 96 and later, the weights moved to the flexplate.... so, you should have none on the flexplate, but at least one on the converter. Or might be weights on the flexplate, and none on the converter.... If there is a mismatch.... I suspect one bolt will be missing, or the bolt hole will show evidence of being drilled on....

The fly wheel is part of the converter on my trans, I was going to have him run the engine when the trans was out but he couldn't, no flywheel without the converter all one piece.

How do you bolt it to the crank then???

Looked it up...... There is indeed a separate plate the converter bolts to..... At least, there should be...... Have a look here.