Change programatically pin number in shield software library?
Some libraries are written to accept pin numbers as arguments to the constructor (Adafruit's library for their MAX6675 thermocouple amplifier, f/ex), but since a shield is normally expected to be connected mechanically (and therefore, to a known pin configuration), there wouldn't be much point.

You have access to the library source so you can make a version with your custom pin assignments.  For a little more flexibility such as you're asking about, pass the pin assignments to the constructor as parameters.