Amazing. Is it hard to get the panel lines to match between layers? Visualizing the process makes me think it would be tough.
It is not that hard really. This is how I do it using Paint Shop Pro but I imagine other programs would work in a similar way.
What I do first is save a copy of my finished skin file, in this case "B239.psp" as "B239_B_a. psp". I make the bump map the same way except saving the file as "B239_B.psp".
I then make this new file into a greyscale image by selecting Image/Greyscale in the menu. Now I have a multi-layered exact copy of my skin in the greyscale format that the spec map needs to be. Next I make the background layer black and the various paint and materials layers that I don't delete above that white. The opacity of each of these layers is adjusted to get the shade of grey I want, so the camo paint layer might be 8% opacity, the tyres 4%, the bare metal 50% and so on. Above these are weathering layers, panel line layers, rivets, small parts and so on. Most of these are turned black and the layers' opacity adjusted to taste. Paint chips are turned white and turned down to around 40-50%. Once I'm happy with the result I save the file as a bmp and check the effect in the viewer and readjust the layers as needed. Then I keep doing this until it looks right, with a final check in the game.
What helps me do this quickly is that I plan the basic skin with the spec and bump maps in mind. So for instance I have a layer for holes in the skin and another for landing lights etc. On my early skins I'd have combined these both onto one layer. However in the spec map the holes need to be black as they don't reflect light at all and lights close to white as the glass reflects very well. So making them seperate layers in the base skin file saves some time in making the spec map.