I'm just grasping at straws here but is it possible that the geometry of the linkage to activate the clutch has changed with the new engine. What if you were to install a longer or shorter rod somewhere?
1953 Chevrolet 3600 Fried Green T'mater (Vern) In the Stovebolt Gallery Caution: Political Statement Man who runs in front of car gets tired, man who runs behind car gets exhausted.