svkd, sometimes we slide the hubs down the shaft just a bit, a guy could make up the difference if there were enough room on the shaft, and move the pump hub a bit and the motor hub a bit.
The way we do this is fab up a rigid plate you can bolt on the hub, and make a spacer of the desired adjustment, 60 thou or whatever you want. then you start to apply torque to the plate and the hub starts moving. Sometimes it doesn't move and you can apply some heat to the hub to loosen it up. It depends on the pump.
This fix has to be agreed upon by the owner of course. Also, vendors don't always give you couplings that fit, and when you call them out on it they will tell you to move the hub. Additionally, some flexible couplings are pretty forgiving. Check the coupling against the data sheet to make sure it matches, and see if you can find a tolerance for axial distortion for the coupling.
Let me know if something here doesn't make sense.
In my experience, as long as most of your hub is on the shaft you are ok. This is subject to owner's approval and they will decide if they take it or not.