If nothing unforseen happens in my scedual, i will finish the ship and send You the files by tomorrow evening. I had however to make changes to Your UVW Mapping, so You will have to redo the Hardpoint Dummies and export the ship to tha game again - if You like the result.
As for a quick pointer... I believe Your problem is more about the unwrap, than actual painting. In general i believe that - at least with low-polygon models - the UVW unwrap is the key to a good look.
Yours was too cluttered - too many small pieces, from surfaces which actually should have stayed together. (I was also wondering if You was using some kind of script to make the unwrap ?)
You should try too keep as many faces connected as possible without distorting them. Ideally - but not necessary - also keeping them roughly the same scale related to each other, as they are in the model. And - at least with large parts - also in the same orientation (Especially when planing to use normal map on the model).
You also can save you some work, when placing similar or symetric parts over eachother - then you just need to paint them once.
When You manage this, painting the stuff is not a big problem - if You know how to produce simple geometry in photoshop or what ever software You like, You will be able to achieve good results.
To illustrate what i mean...