Cleaning up 4.8V and 10.8V DC power affected by spark ignition system
Basis for my unfounded assumptions: I think the magneto is flooding the engine assembly with noise. It isn't dissipative, and there is no connection to a larger ground. Given the insulating nature of design, not even earthed when landed. It's just one side of a circuit with big spikes on it.

So:
Don't earth  your battery powered modules to chassis. You know it makes it worse.

Float the modules, make Faraday cages for the electronics modules and use screened cables for your interconnects.
Use the outer screen to connect the Faraday cages.
Connect the screen at both ends.  ( contrary to normal practice.)

Float the electronics from the Faraday cages.  Currents from the magneto and other RF sources in the environment are not wanted. (you will pick up plenty of RF once you get airborne)

Lightweight Faraday cages can be made from plastic enclosures and much conductive screening spray. ( generally on the inside, where it doesn't get rubbed off)

Where possible use transformer isolated differential signals between modules.  Single ended or ground referenced signals will be problematic.

Shared power supply will cause problems, assume the power supply is a noise source.  Try at least common mode chokes at the boards.
In noisy mobile systems there isn't a convenient chassis or ground to bypass power line noise to.

Antenna feedthroughs are problematic. 

Military solutions to this kind of problem involve screening the noise sources as well. ( see the comment about Fitted For Radio (FFR) vehicles).