OK, so I've fitted new seals to my water pump.  Both seals are perfectly seated and the shaft was pulled through very carefully.  Everything turns with just as much stiffness as you would expect.  

However, the drive gear is not perfectly flush with the casing all the way round.  In some positions it is slightly below, in others slightly proud.  If I use a washer in order to pull the shaft in further, the inner face of the gear will touch the pump casing (verified with a feeler gauge).  

Obviously the shaft is only seated in the pump end at the moment; once fitted to the engine is it likely to align itself the first time it runs, or will it knock seven bells out of the inner casing?

Just as an aside, where the half moon cut out is on the engine, there is no corresponding hole or channel on the pump side.  The pump casing is blank.

The gear is very close fitting there will probably be only 0.002 in when it is bolted up so if you can fit any bigger feeler gauge under it, it needs to go in further.

Thanks, I've just checked and in some positions it won't take even a two thou feeler gauge.  I have just noticed that in the positions where the gear stands proud, a little inwards pressure will temporarily correct this.

a few of us were discussing that half moon bypass

after seeing another water pump and examining it closely

I think we decided that the bypass valve relieves the high pressure side of the pump ....to the low pressure side of the pump rather than back to the sump

this might be different in some early versions ...but this appears to be consistent across the years 86 and on

Well, RicK G was correct.  Despite the tiny clearance on the inside of the gear, I decided to use a washer to pull the shaft through a little further and it worked.  If there is any interference between the pump gear and inner pump face I can't feel it.  So many thanks for the solution.