Q: Trans is making a loud clunk when I put it in drive

If there are faulty motor mounts those should be repaired. Once that repair is made, if the noise persists, a noise of that "type" is often due to faulty axle joints. In your circumstance, though, inasmuch as work was performed on the transmission, it is possible that there is too much "thrust clearance" in the drive train and/or parts were installed improperly or even left out. Transmission repair is very exacting work; the work must be performed perfectly in clean room conditions. As you describe it, the noise sounds quite evident (marked) and so on direct inspection a trained professional will surely pinpoint the origin of the noise. If you desire a definitive diagnostic, please use YourMechanic’s vehicle noise diagnostic service request page and the responding certified mechanic will definitely find the origin of the noise and explain your repair options in detail. If you have further questions or concerns, do not hesitate to re-contact YourMechanic because we want you to make the most of your repair dollars and help you to get the absolute best possible results.