Diagnosis help please...

Trying to diagnosis my 1986 Delta 88. The car only has 52k on it. When I bought it, it had a hesitation from a stop, slight stutter at a constant speed (between 40 and 50) and clunked around putting it in gear from reverse or even just in drive in some cases. Also it clunks and shakes when it shifts gears in normal driving. It had a bad CTS and I replaced it. This seemed to fix the erratic idle (for the most part) and it no longer is hesitant from a stop. A few months ago I also had the TB off and gave that a nice clean right before some GM top engine cleaner. However, after doing the CTS a few days ago, the stutter at a constant speed seems to be worse and more frequent. From what I can tell its most common around 45mph. I thought maybe it was the converter locking up for OD but i leave it in 3rd gear and it still does it.

The clunking around I'm almost 100% sure is bad motor mounts. Anyone disagree? As for the stutter and shaking around 45 MPH, I'm thinking maybe a vacuum leak? It still does have a slight erratic idle (was thinking the IACV could be dirty) but haven’t had time to pull it and check it. I'm hoping with 52k miles on it, it isn't a trans problem but i could be wrong. Any ideas? If you need any other specific information, please let me know.

Thanks in advance,

The Clunking Could Be A U Joint Or As You Think A Motor Mount. The Problem With The Motor, I Would Check Two Things Right Away. One Check The Rotor Make Sure It Isn't Burned Through To Ground On The Distributor Shaft. If It Is Black Or Dis Colored It's Burnt Replace It. Second Make Sure The Two Wire To The Pole Piece(pickup Coil) Which Are White And Green Are Not Broken. If So Replace The Pu Coil.
One More Thing, Yes You Could Be Correct About A Vac Leak And It Would Be Around The Carb Base Or At The Egr. Repair Or Replace Defective Part.
Hope This Gives You Some Things To Look At.
Ron

The Clunking Could Be A U Joint Or As You Think A Motor Mount. The Problem With The Motor, I Would Check Two Things Right Away. One Check The Rotor Make Sure It Isn't Burned Through To Ground On The Distributor Shaft. If It Is Black Or Dis Colored It's Burnt Replace It. Second Make Sure The Two Wire To The Pole Piece(pickup Coil) Which Are White And Green Are Not Broken. If So Replace The Pu Coil.
One More Thing, Yes You Could Be Correct About A Vac Leak And It Would Be Around The Carb Base Or At The Egr. Repair Or Replace Defective Part.
Hope This Gives You Some Things To Look At.
Ron

Its an EFI system with no distributor.