Ah, I see. Well, I think the only thing I did besides editing the .exe was add the shuttles to the defaultcore and defaultloadout files (with Class set to "SH" in the defaultcore file), like you would for any other ship, just make sure their names match the names hardcoded in the .exe (or change the names in the .exe).
You need my mod to get all the 9 races working with the ships and stations I gave them. But you could easily make different ones and you can change the full empire names in the RaceNames.gf file (most of the game's files only use the short empire names). What's more difficult is setting up a conquest campaign with extra races. You need to run a copy of Windows XP (a virtual XP copy works as well) and create a new map. You also need to create new scripts for the scenarios. This too only works with Windows XP (you need Visual Studio 6, modern versions won't work, and have C/C++ programming experience, which I did, but I still barely understand the basics of the structure of the scripts so don't even go there if you don't have programming experience), though you might get a lot done by simply editing the names of ships and stations in the scripts I put in my mod (open them with a hex editor or maybe even notepad and look for the names). I spent a godawful amount of time making this mod and its patches (it's a miracle I didn't lose my job or my girlfriend), I'm still proud of the result but I wouldn't recommend starting from scratch unless you're gonna be stuck on a deserted island for at least six months, but like I said you might get pretty far by just changing shipnames, textures, etc... in my mod, for which you have my permission as long as you credit me in the readme of the end result.