Hi @qnguyen, welcome to the forum 
While their input and output functionalities are similar, the Navigator and Pixhawk1 are different devices, and have different hardware that needs to be configured.
I asked internally what the process is for building ArduSub for Navigator and was told it should be the same but using ./waf configure --board navigator instead of ./waf configure --board pixhawk. You can use ArduSub-beta to checkout 4.1, although you seem to have figured that out (or something equivalent) already
On the file type, instead of the .apj files that we generally use for the Pixhawk,