Hi @willronan -
You can provide 5V from the fuse board, but the signal from the Navigator is 3.3V. Are you saying you intend to switch 5V going to the pump, via the FET?
If the pump motor is only 5V, it may be preferrable to use another controller that does use servo-style PWM input? Is the pump brushless or brushed DC?
See this thread for info on how to configure the output to be non-servo style PWM.