Hmm.. Just download Harpo's stuff for now as they're already in text format. Worry about getting ConvertData to work later.
Stick this in whatever folder you want, though make it somewhere easy to get to.
After that, go into the game and click options->mods->mod path. This will create a mods folder called Mods-Rebellion vX.YZ. This is the location:
C:\Users\<your name>\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Mods-Rebellion v0.96\
That location is where you should put your mods. To create a mod, go into Mods-Rebellion vX.YZ and create a folder by whatever name. For you, let's make a folder called "Advent Super Capitals." Inside that, make a folder called "GameInfo."
Now, copy the Advent capitalship files from your reference folder into GameInfo. The files you're looking for are...
Now that you've copied the files from your reference folder to ...\Advent Super Capitals\GameInfo, open them up. Scroll down until you hit NumWeapons <integer>. Below that, you'll see the various weapons that ship has. Increase the damage numbers to something absurd, say 9999.999999. Then go back up and increase the hull/shields. Repeat the process for the other files.
Congratulations, you've made your first mod! Load the game, go to options->mods and click on your mod and click enable. This will stick your mod in the second list box. Make sure the checksum isn't zero and if it's not, click Apply. Play game as Advent and watch as your new super capitals trounce everything else in your path.