Q: Vibration/chopping sound

Ok, so, my truck has been smoking on start up for a few years now and me and my mechanic friend decided to fix it. We pulled the motor, replaced valve stem seals, headgaskets, valve covers, water pump, timing chains, and radiator while at it. We also cleaned and degunked the pistons, oil pan, and heads. We set it to TDC, put it on time, and reassembled the motor. Then we put it in the truck and hooked everything up.

It started and ran perfectly. we then checked the oil and transmission levels and had to add about a quart of tranny fluid. I then took it for a test drive and was easy on it for about 20 miles. I then got on the throttle pretty hard and it started making a slight chopping sound and started vibrating more and more the higher in the rpms I got. It shifted smoothly so I don't think it's the tranny. However, after it shifted and I stayed on the throttle it would immediately begin making the same noise and vibrating again. It never did this before. What is wrong with my truck?

My car has 134000 miles.
My car has an automatic transmission.