Was the clutch removed during the engine swap? One common mistake on assembly is putting the clutch disc in backwards so the springs in the center hub catch on the flywheel bolts and cause the clutch disc to spin even with the pedal fully depressed. If you force the trans into gear, or engage the transmission with the engine stopped and start the engine with the clutch pedal down, a backwards clutch usually makes a rattling noise as the springs rub the bolt heads. A bent disc, as Kevin describes is also a definite possibility.
Remove the dust cover and look up at the flywheel/clutch assembly while a helper holds the clutch pedal down. There should be enough of a gap between the pressure plate and the clutch disc to turn the disc easily with the tip of a screwdriver. If not, either adjust the linkage for more clearance, or take it all apart and look for bent, damaged, or improperly installed parts.
Jerry
