Firmware for a Research VTOL Prototype

I’m a PhD student and a PX4 beginner working on a novel VTOL Tailsitter prototype. I am trying to fill the gap between writing equations (to describe my system model and control system), and implementing them on PX4 hardware. I already managed to fly my prototype by modifying existing PX4 airframes. I learned how to add an airframe to PX4 and modify the mixer and geometry files…

However, I would like a more methodical/systemic approach where I can make sure the only control system running is one that I designed, coded and fully understand.
In other words, I’m not an expert on everything going on in the source code. What would be a good strategy to have a minimalist basic clean developer workspace where I can develop code to run only on my custom airframe?
My intentions are to experiment with different control strategies.

Hope my question is clear.

Warm regards