Ok, so here's a couple screens showing my first crack at replacing the icons...
As you can see, It wasn't entirely successful..
I modified the Unit_Main.tga file like so....
Based off of the data in the from MainViewIcon-Ship.brushes file
...
brush
name "MAINVIEWICON_CAPITALSHIP
_TECHCOLONY"
content "Simple"
fileName "Unit_Main"
pixelBox [ 1 , 91 , 28 , 28 ]
I assumed that since my replacement icon fell entirely within the 28px by 28px field defined in the .brushes file that everything would pull through...
However, as you can see in the screenshot, the ship icon is still being rendered using the same transparency mask. I haven't been able to figure out which file contains the mask yet.
If anyone has any information about editing the transparency mask for ship icons, I'd really appreciate the info. I intend to create at least one complete set of icons that are more abstract and functional rather than tiny 2d sprites of the ships.