Separate calibration values from program
What you really want to do IMO is identify each pump, and keep your  software identical for all your devices.
In the past I've used Maxim 1-wire devices which provide a small amount of storage and a globally unique ID.
You could store your PWM value in a 1-Wire device and make it part of the pump or it's cable (the 1-Wire device needs no power supply). It means you have two extra wires running to the pump or you could even fit the 1-wire device into the pump connector and avoid extra wires. 

Look at the DS28E07 device which has 1k of local Eprom storage and costs a $1 in TO92 form factor and 1 off qty.

The interface is a simple two wire (sense and ground) system.