You need XSI. While you can model ships in any modeling program. you MUST have XSI to finish your model, and make it ready for import. Version 6.0 is what the developers used. Mod Tool is free, and will work, but its a little more of a challenge to use.

Photoshop, or equililant for texture editing. It must be able to read, and save dds, and edit the color/alpha channels  Most use Gimp if you are looking for a free program.

For  the Game info, stats, ship, and player entity editing etc. etc. all you need is trusty wordpad. Though you may want to use Harpos tools (can be found in the 1st few pages of these boards) to convert vanilla sins entitys from binary to text first.

Read the mod documentation that comes with the forge tools. While it doesnt cover everything it explains much, and what it doesnt explain you can usually find here..