Q: MDX 5 speed auto transmission, when drive from 20 to 30 mph, shift cable shaken at D5, transmission makes click noise at D4 or D3

If the issue did not exist prior to the rebuild, it is likely the transmission was not properly rebuilt (not unusual because rebuilding a transmission is highly detailed, exacting work, plus a really good rebuild will incorporate all the design and part updates that often are available based on years of field experience with the transmission and feedback from MDX owners). If the re-built unit has a warranty, obviously make a warranty claim. As far as the technical causes, noise and vibration could be due to issues with the torque converter and/or converter lock-up (was a new converter installed or if rebuilt what vendor was used?; not all converters are equal in quality) or the noise/vibration could be due to mechanical part failure, imbalance, or even fluctuations in hydraulic pressure, again due to defects in the rebuild, improperly fitted parts and so forth. Using a real time scanner that can capture transmission operating parameters might narrow the diagnostic but in all likelihood if you are hearing actual noise and/or vibration from the transmission, it will have to be removed, disassembled, inspected and put together properly according to the instructions and incorporating all current updates, of which there are undoubtedly many. If you want this confirmed, including finer pinpointing of the root cause, the recommended service is a vehicle vibration/noise diagnostic - transmission suspected fault. If you request that service the mechanic will get this resolved for you. If you have further questions or concerns, do not hesitate to re-contact YourMechanic as we are always here to help you.