I think you need to put an angle finder on the trans output shaft and the diff yoke to find out if they are parallel. You also need to determine if the centerline of the motor/trans is parallel with the centerline of the car. You can move the motor/trans a little to the passenger side to make clearance for steering for instance, but the crank centerline must be parallel with the centerline of the car. If the angle of the front u-joint does not match the angle of the rear u-joint in both planes, you'll have problems. Look at the front as having a positive angle and the rear as having a negative angle. They must be opposite but equal and cancel each other out.