Re: Portugal has two of every ship available, any idea how to fix?
I think you're right that the problem is that Portugal has access to generic ships and their own. When I modded Empire Total War to add ships for minor factions, I sometimes saw that side-effect (that some factions could recruit two versions of the same ship) - this is listed as a known issue for my Minor & Emergent Factions Unit Pack (which means that I noticed the problem, but didn't find a solution, unfortunately).
It might be possible to edit a Darthmod file or to create a separate mini-mod that would avoid this. However, I can't tell you which Darthmod file to edit and I can't guarantee that (even if you know which file edit) this will work. The method that I used to prevent factions from recruiting ships was to limit recruitment of that type of ship to a land-locked region (to create mods to prevent the recruitment of bomb ketches and rocket ships), but obviously if you did that for the generic ships, most factions wouldn't be able to build fleets!