Navio2 + APM for estimation only

I have a Navio2 which I am planning to use to supply state estimates to custom control code. Thus far it looks like this should be feasible by hacking on the Ardupilot code, though as I’ve started to look at it in more detail I have the feeling it may be quite the rabbit-hole.

So before going much farther I’d like to get some expert advice: Is what I’m proposing the most direct route to obtaining a full-vehicle state estimate that can be input to my own controls code, or is there a more elegant way to make use of the Navio2 hardware?

Does this seem like best course of action or are there existing projects that are closer to what I’m looking for: something equivalent to the vehicle state estimation portion of Ardupilot (not control, missions, RC or anything else)? And either way would having Reach hardware in addition to the Navio2/RasPi3 make the task any more straightforward?

The Reach seems like it almost provides what I’d need though I think the crucial step of “IMU integration” (using the terminology from the roadmap) is missing, so I’d still need to borrow an estimator (i.e. probably an EKF) from somewhere, hence the need for Ardupilot.