Another possible scenerio: IF the C-C dimensions for the shaft were stock length, and IF the replacement yoke was the same dimensions, and IF the Engine/Trans is in the stock location, then basically you only have 2 possible culprits for the shaft to be too short. The first would be the "stacking" of factory tolerances, the second would be that the rearend housing is not in stock location- perhaps the locating pin in the leaf springs has sheared. In the "olden days", we often redrilled the front spring hanger to shorten the wheelbase slightly, and flipped the front brackets upside down to lower the rear of the car and move the instant center up.

Also if the body is bent even slightly it will change the length between the trans and diff. If it is bowed down like a smiley face the way it would be inclined to do after sitting on the wheels for almost 40 years then it would need a longer driveshaft.

Production tollerances could stack up quite a bit, think about the perches could be a hair off the body seams could be a hair off.