as far as the three-light setup goes, you don't really want it to follow the plane, as no lighting setup actually follows an animated object... the animated object flows through the lit environment. having lighting follow an animated model will appear very unrealistic.
for the runway light flickering, try going into the graph editor, selecting your entire animated curve (which i'm assuming is intensity) and copy it (with ctrl + c), then paste it(with ctrl + p) in the graph editor with the other light selected. i can't tell if this will work, but it's all of about 5-10 seconds of work that may or may not help. may as well give it a go.
as for the lights to be added to the plane... open your hypergraph, and then try selecting your lights. if you have your wings grouped or parented under something else, the hypergraph will show you... middle mouse (MMB) drag your selected lights (that you want to add to the plane) onto whatever is at the top of your plane's hierarchy. that should attach them.
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