Trashman, I will say, having actually seen this thing's geometry, that you are still making waste of a ton of polys because of all of your square details that aren't aligned. There is no reason that a ship of this complexity should be registering at over 3000. That said, I have some basic shots of the mapping that I used.
I didn't finish mapping it because the geometry is an absolute nightmare to come to terms with for texturing; and because I've lost the original mapping and texture groups in conversion I just wanted to quickly point out some suggestions.
First, the turrets. Disregard the style of the turrets I plopped on as deck guns; they are the turrets I'm using for my terran fleet and I had them handy. Yes, they are a couple of hundred polys each, but they are also single texture and are thus highly optimized for HTL. With the SCP we can specify a starting rotation for things, so depressed turrets (and those rear-facing ones) need to be done to not look stupid on a ship this large. Anyway, the big point there is that they aren't technically tile mapped (ok, so those actually were before I baked the texture as I'm sure someone will point out, but even then they still weren't a single overtiled texture) and that there is detail in them that will be important when they are blown up to several hundred meters long. Make the small turrets more detailed as well; 10 tris isn't worth rendering the subobject, quite frankly, and those squares have to be huge given the rediculous size you're assigning this thing.
Second: contrast. I changed the base texture because the one you were using (either TCov1a or Capital7) is probably the most hideous of all the stock freespace textures when tiled (it's not seamless top-to-bottom, so it bands like hell), but I also took the step of changing the central structure to a different texture than the main hull, and one with a fairly large contrast to said base texture. This is important, because it visually sets the superstructure apart from the mass of the hull. The rest of the plates I also made darker; I didn't bother with the gaps because you've already got those mapped on the original and I think they stand out fine as they are. But change them to a darker texture as well and they will become much more apparent.
Finally, I'd like to give a few critiques of the model itself. For all of the so-called detail this ship has, it's got a lot of places that are quite frankly boring. The fact that you've got as many polys as you do but are still using 8-sided engines is one big point, you can afford a few more polys there at the expense of some of the little recesses and bumps that don't contribute in the grand scheme of things. Also, those square headlights on the front just don't work, so think about what options you have up there.
