im not very sure, but im guessing you need to configure your encoder pulses as 1440 (or 360 x 4)
Since it is most likely a quadrature encoder, it will output 4 pulses per count...
or something like that.... i read it somewhere a while ago hehehe....
post some pics of the completed progress... and if possible a video, it is great to see mach3 in non standard applications
Best regards
Fernando