I had a similar problem on my 48 after replacing engines. It turned out that the bell housing wasn't centered with the transmission. I talked to a old mechanic from the late 40's. He told me it was a common problem back then. GM had a special tool to line the bell housing to the fly wheel. You would remove the dowel pins between the engine and bell housing loosen the bell housing bolts, install the tool then tighten the bolts and re drill the dowel pin holes to a larger size. Of course not able to find the tool he had me remove the clutch, place a magnetic dial indicator on the flywheel and center the transmission hole to the bell housing. Tighten the bell housing bolts and re drill the dowel pin holes to a larger size. It was out about .020.That was back in 1980 and it still works today. I also learned the pilot bushing is oil-impregnated and using chassis lube will make it stick.
