Here are some ideas:
1. Make sure your aircraft forms a Faraday cage
In aircrafts as in cars the conducting surface is the most important protection for inside matters (people and systems). If the airfraft is made of glass fiber for example and does not have any natural conductive surface, then such a conductive layer (or arrangement) is made.
Make sure that the layer is able to conduct the currents in a lightning. For example a copper wire having a diameter of 10 mm is able to conduct most lightnings without damages.
2. Make sure that nothing important is outside that cage
This is important. If you have for example some aircraft light in a plastic holder on the wing tip, it will be an invitation for the lightning to come inside the plane and destroy something. In such a case wrap the plastic holder around a copper cable and connect that to the airplane surface (to the faraday cage). Try to arrange the internal conductve parts so that there is always some surface grounded parts in front of the part that will conduct the lightning to the surface away from the lamp holder and internal wires.
3. Do not ground anything to the surface (Faraday cage)
In cars it is common to ground everything to the vehicle steel frame. Don't do that in airplanes. Opposite to that keep the parts and wires at some distant from the faraday cage as seen in the video above and the picture below. The cage works but only if the parts are not too close to it.
Picture: Keep distance to the surface (which will conduct the huge currents of the lightnings)
No groundings! How to arrange the groundings if one cannot be avoided. Inside the faraday cage the best is to have a single ground point that is NOT connected anywhere to the cage as in this video.
The person keeps his hand on a bar that is no conductive. This way only the shoe bottoms are grounded. Make sure there is never a ground loop anywhere. If an ground loop exists then the lighting might choose that way and it will put a huge voltage into that system destroying something.
5. Use transorbs everywhere
If the system is 12V DC battery, then use for example 18 V transorbs everywhere to protect the circuits. Remember that if you have a long wires to some part then both ends and maybe even somewhere between needs to be protected.
6. Shielded wires
Shielding does not help if the faraday cage is not working. Why? Since the shield will be the lightning conductor and the shielded system is mostly destroyed anyway if the lightning hits the shield. The shield helps to give more protection if the surface faraday cage is working and keeps the lightning outside the internal systems. Better to conduct it away (see section 2.)
7. Avoid lightnings and surges
Try to avoid thunderstorms and lightnings. The best surge is a surge that never happend.
Notice: The windows do have conductive layers so that the cage is complete.
Here is a small article about lightning protection in a composite airplane.
NASA made some airborne lightning research 1980-1986. Here is a video about those tests:
At 4:42 notice how it strikes inside the cockpit to the pilot (or looks like so).
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