OK, I'm stuck. I have replaced the oil and water pump seals for the second time (1989 K100). The second time everything went according to plan. And then I noticed. The pump drive gear is flush with the pump face, or even slightly recessed. Until I turn in through 180 degrees, when it is standing slightly proud. So it's flush on average :yes The gear shaft is in very good condition.
On the inner side of the gear the gap is less than 2 thou in some parts of the rotation, slightly more in others. Everything turns as freely as you would expect.
When the gear is standing proud, it is possible to temporarily press it down flush. Is the gear likely to line up when the case is tightened down, or is it more likely to bind on the engine case? I don't really see how the fitting of the seals can be at fault, as there seems to be some play in the mechanical seal that would allow for sideways movement anyway. However, I would be happy to be told I'm wrong, at least it would be a way forward. When the pump is offered up to the engine, no gap is visible to the naked eye between pump/engine.
I have searched for answers to this, but found none.