The measurements will depend on if the body is still resting on the subframe (through the subframe mounts). If you're doing this with a lift and the front subframe/suspension hanging, then the geometry could be different (depending on the condition of the subframe mounts).
The engine/pan geometry with respect to the subframe can be affected by:
- the condition of the motor mounts (affects the vertical distance of the engine to subframe)
- the condition of the subframe and transmission mounts in combination (affects the engine 'tilt' angle)
What I understand from your description is that the engine [as installed] is not completely in-line with the driveline of the car? (assuming subframe is exactly perpendicular to the driveline). There are many variables here. Whilst you have the engine out, make sure the subframe itself is not warped (procedure is in the BBB), and that the subframe alignment is correct (through the front leaf-springs).