1) 'Skin Effect'. When AC current flows in a conductor, it tends to concentrate at the surface of the conductor. The amount of concentration depends upon frequency, and can be described in terms of the 'skin depth'. Skin depth is shallower at higher frequency, and for 3500 Hz, the skin depth is about 1mm. Wire resistance will be higher than you expect. You may need to parallel conductors to avoid excessive skin effect.
2) Transmission line effects. All cables have capacitance. All cables have inductance. The effects of capacitance and inductance become more noticeable at higher frequencies and longer lengths. I don't know if this is a significant issue for your application.
3) Ignoring the above, at 5A and 240V and 3500 feet, you will need 4ga copper in order to keep losses below 5%, by just 'ordinary' voltage drop calculations. $5K in wire to move 1KW; payback won't be quick. Can the alternator be wound for 480V?
-Jon
