I thought I'd done a final wrap up on this thread long ago, but stumbled on it again. Well here it is (for those who might find themselves in the same predicament)...
Car is driving wonderfully, now. Some of my transmission problems were due to the fact that I had totally ruined the transmission by foolishly towing the car on its back wheels. The long dolly tow behind my body shop guy's van with the rear wheels spinning completely overheated and cooked the transmission. The only thing that saved me was the generosity of the forum member who bought the donor car from me offering an execellent price on selling me back the transmission installed. I did not have the heart to do it myself and the price was low enough I could live with it. I chalk that particular bill up to my own ignorance, not the wreck or the body guy towing it. I helped load the car on the dolly and should have known better.
The last of my "clunk, clunk" problems were that both motor mounts were broken. On one side, the aluminum dome on top of the rubber isolation bushing was shattered so the bolt was free to pull out, and on the other side the "support arm" that comes out from the engine to connect to the motor mount was broken off at the end. Motor was just sitting in there. With the mounts replace, no more "clunk, clunk" and I now have smooth shifting.
Interestingly, the car still "slams" into reverse with a hard clunk when the car is cold (chirps the tires), which I once thought was the transmission but now that I (for other reasons) had to replace the transmission it does exactly the same thing.
My Maaco bargain paint job looks good and has not (yet?) started to flake or peel. Good thing I had the whole car painted because it is definitely a subtly different color now (a little darker), but I like it.
My water pump started leaking and I replaced it. Might have been wreck related, maybe not.