If I am reading this right, the new system base timing is verified by 'locking' the timing in the software at 12* and verifiying on the damper marks with a timing light.
But that is a different matter from locking the mechanical advance mechanism in the distributor. Is this the stock distributor being used for this new system, or a new distributor being provide with the new system? I guess this is a dumb time to ask this but what EFI system is this? Pro Flo 4, with a new distributor?