I have done the 200R-4 install in to my 65 cloned GTO. The darn thing makes a very noticeable KNUNK when I let off the gas. Tonight I have it up on jackstads with all 4 off the floor and I can here it from about 30 mph and up but not as loud, until I let off the gas. At first I questioned the rear end but not sure now. Last weekend I changed the U-joints hoping to cure the noise, nothing changed. At the front yoke I have quit a bit of up and down movement but checked my other car that has the same trans and it has about the same play. I even tryed the other cars yoke in this one and the up and down is about the same. The other car has no noise in the drive line at all.
All the stuff I have read on this swap nothing is mentioned about the Pontiac flex plate space to the converter. Other GM cars (Chevrolets) the flex plate is stamped back toward the coverter about 1/4" for bolt pads, but the Pontiac plate is flat like the Buick and Olds motors this trans was also used in. I'm hoping the tail shaft bushing isn't the problem because this trans case is one piece.  

I would suspect the rear end to check for a clunk sound put both rear tires back on and drop the rear of the drive shaft and turn one of the rear tires back and forth to see if you hear any noise or feel any major slack if so than it is most likely the ring&pinion or the spiter gear assembly.  

I had it and took the rear end out and took it to another shop that has a good local reputation. The first thing they did was pattern the set up, and said the first guy missed it completely. When the tech unbolted the carrier it feel out, no pry bars required. The pinion was .020 short and the ring needed .018 on the right side. So no matter how good a job a guys talks the proof is the results. Nothing new for this project though about everything has been done at least twice.
Thanks for your in put. Next I'll reinstall the rear end and keep my fingers crossed.