Barry,
Congrats on your entry to Pagodas!
I would say that the Auto box should not be rough. In fact, when all things are "tuned" I find it surprisingly smooth for a design from 50 years ago. I am in no way an expert at these but have done a couple things that changed the shifting.
1. you must make certain that your fuel/air linkages are correct - this is very important and makes a significant difference in shifting due to item 3.
2. you need to make sure that the motor timing and such are correct.
3. there is a little solenoid switch on the throttle body (air intake) with a couple of wires on it. If items 1 & 2 are adjusted correctly and the transmission still shifts rough, you can adjust the position of this switch as it will adjust when the trans will shift. A very tiny (hair) movement makes a change in shift timing. Don't do this until you have done items 1 & 2.
4. If shifting has improved with the above crucial items, BUT you still hear a slight clunk, check the rubber differential mount that comes up into the trunk. When this mount is metal to metal, you could get a clunk.
you will also read about checking the solenoid on the trans - I will not comment on that as I have not had to do this. The above 4 items were enough to get smooth shifting.
Some links that will help:
https://www.sl113.org/wiki/Restricted/Linkage-tour (must be a "full member" to access)
https://www.sl113.org/wiki/Automatic/Start#SmoothShiftinghttps://www.sl113.org/forums/index.php?topic=806.msg3842#msg3842 (for the Diff Mount)
There is more than this, but this will get you started and all of the above is easy to check.