Charlie, it sounds like you have the correct steps. The most important ones are 4 and 5. Maybe try emptying your \PaintSchemes\Cache folder just to make sure? (When a skin is loaded, it creates copies in .iga format the cache folder, which is what the game engine actually uses)

I don't know but it might be simpler than that. Selecting a skin in the fmb does not work for the player's plane. You need to select it in the arming customization screen before you hit "Fly".
I thought my game was broken the first time I tried to make a mission, only for my skin not to appear.

That's how it worked always. And if you selected a player's skin the game will use it each time you are flying the same aircraft type.

ATB
Armin