Take a look how it is done with stock sh4 textures. There is black&white diffuse map in AO alpha channel. So, take your ships texture, make it black and white, adjust it with the "curves" option (in Photoshop), so it lt looks dirty, then copy it and paste to AO map alpha channel.
I dont know how to do it in paint.net, you cant probably, but it should be possible in gimp.
(Get Photoshop cs6 30-day trial + nvidia dds plugins and you will do it in 1 minute,
that gimp is piece of ... something rotten 