Well, luckily for you, this is pretty easy. What you need to do is create a new shiparch.ini entry through XML, that is identical to the original in every respect except for the stats you want to change and (this is the important part) with new Name and Info strings. Go download my XML Toolkit Mod to learn more about how to do this- I put Juni's Defender back into FL, for example, and the CSV, etc.

FL will put up with more than one INI entry making use of the same CMP references. You could even add Hardpoints to the ship, and just add the Hardpoint references to the "souped-up" version, for example. What it won't do is let you keep the same Name and Infocards. You'd need to implement them through XML/FLMM or by hand-editing a DLL.

But... at the risk of sounding like a priss... what's the point of having a ship that looks the same, but is functionally different? Seems to me that that would mainly confuse players... I'd go the whole route, and export the CMP/MAT and alter it so that it looks different enough that people can tell them apart...

well the interesting use that comes to my mind first is lying shipdealers - they say you're getting a newly minted whatsit & you get a lemon - makes real experience/knowledge more important,i.e. don't buy your ships at X they skimp on the hull armor thus the unbelievably low price etc