Colin,
The end float of the pump shaft is NOT controlled by the position of the drive gear - there is normally a gap of just over 1/8" between the gear and the top of the pump body. The end float is controlled by the fit of the head of the pump shaft in the pumping chamber - the depth of the chamber should be the same as the depth of the head - the paper gasket on the cover plate provides the running clearance for the pump.
If your spare pump has been machined out to give greater output, other problems may arise. The vanes having more travel will mean the spring is less compressed, so not exerting as much pressure, with the possibility that some oil could escape past the poorly seating vanes - resulting in more theoretical output but less pressure.
Regards,
Eddie.