Hi Col,
The three pullies must line up 100% or as close as you can get it. Otherwise it will damage the fan belt, possibly damage the water pump and/or alternator bearings or, least of all, the belt will squeal lke a stuffed pig.
Although we know exactly what you are talking about, your picture does not show us the problem clearly. Try to shim it, fore or aft, with a washer or two. See if you could get us a better photo of the alt, the belt and the water pump, showing how they line up.
Regards
Chris
Cape Town