GSoC 2018: Balance Bot with Ardupilot

I have this thing, with an Arduino and stepper motors, controlled with an R/C radio. It is driven manually on that video.

What should I do to replace the Arduino with a Pixhawk, maintaining the stepper motors (no encoders)? Is that contemplated in the code?

The final objective is place a RTK GPS and do a mission consisting of laps on that circuit, which is for 1/18 cars (around 2m wide).