I don't see why you'd want to have 3 engines on a plane if only 2 of them will produce power, so it really just is useless weight added to the plane.
And in that motherboard, the Stirling engine itself isn't doing the cooling, the fan blowing air over the heat sink is doing that. The Stirling engine is just converting the heat from the CPU into motion to drive the fan.
I think a more viable solution for the skymaster would be liquid cooling, that way you can place a radiator in a convenient location, or some form of hybrid liquid/air cooling which can be seen on many modified VW
[Edited 2009-01-10 10:24:00]