https://forums.sinsofasolarempire.com/326876
Newbeorg made this, very very helpful, it resizes meshes. First convert your mesh from bin to text, use DK converter to convert from bin to text, once done, resize the mesh you want. If you re-name it something like customcapital, or whatever, then you wont confuse it with the original, or leave it the same name and overwrite the original in the mesh folder. Make sure you make a mesh folder for your mod, and name your custom.entity ship whatever name, list in the mesh call in the entity file and there you go.
If you make the ship too big of course it will overlap the build factory, and you can either say that is ok, or resize the cap factory 2 or 3 times, or whatever... just bigger than the ship and then its cosmetically correct.
Of course lets say you want a ship ten times as big, and resize the factory 11 times, well...
pretty soon, your factory is bigger than your planet.
but the DK converter is here:
http://tgnforums.stardock.com/322559
and the resize tool, is above. Use them and enjoy, and make a cool mod with super cap ships!! 
-Teal