Transmission question.

The lift (or no lift) wouldn't change the performance of the transmission. It will change the driveline angle, which can accelerate wear on the u-joints. Since you felt a clunk, there could be a U-joint problem.

Sounds right to me. The driveline is back to it's original position (angle wise from the tailshaft to the diff). Probably one of your typical shade tree lift kit installs and did not re align the drive line or use slip yoke eliminator creating too much angle (stress) on the U Joints. Surprised you were not experiencing a vibration to boot!!

When I bought the truck it had 315's on it. I replaced them with stock tires before I removed the lift and the transmission still shifted the same. It didn't change until I removed the lift. The truck only has 49,000 mile on it so I wouldn't think the ujoints would need to be replaced but who knows. I crawled under the truck yesterday to see what the shocks were set at. They all arecset at 5. At least I think they all are. The right rear was installed backwards and I can't get to the dial. I'll be fixing that this morning and try dropping the rear down to 2 and see how it rides.

Did you change the tires to a different size when you removed the lift?

Depending on the height of your lift kit and the manufacturer it could have added change of axle angle. There are bolt in shims to ajust the angle of the axle to relieve the stress on the drive line. They could have been left in and need to be removed to match the stock driveline,front and rear axles.The binding of the drive shaft u-joints could be the source of the clunk or the shaft is being jammed into the transmission.You might be able to see the shims near the axle ubolts.
If not that it is a 2001 so replacing the u-joints may be needed.

Driveline angle is critical to smooth operation, but if you were hearing a clunk then you have an issue which the lift exaggerated.

Things to check would be u-joints, center bearing and support (if equipped) and pinion play (which could also be a sign of pinion bearing).

Possibly, if lift was enough to throw off driveline angle, though some 'lift kits' make allowance for that.