Thought it might help to collect SS2Tool 5.0 and some of the more popular SS2 mods and make them be super easy to install, in order to cut down on the confusion and speed things up so you can get straight to playing.

You can buy System Shock 2 at GoG.com and then enjoy the hell out of it. Hope it's useful.
 
http://www.gog.com/gamecard/system_shock_2


Torrent has
-SS2Tool5.0 and its necessary offline install files ready for installation
-Various Mods to improve the look of the game and some minor bugfixing

Mods included are :
+SHTUP- Replaces a bunch of common and not so common objects textures. 
+Four Hundred- Ups the resolution of world textures while remaining faithful to the original. 
+Vurt's Space- Remember how pretty space is? Well now you won't forget. 
+SHMUP- Increases the quality of the music. How? I dunno a wizard did it. 
+Updated Bindings - Not really a mod but applies some more modern bindings to the game.
+Rebirth- Makes many NPCs not look like ass. 
+ADaoB Anomalies, Discrepancies and outright Bugs- General bugfixing mod, but attempts to stay true to the intention of the developers 
+Vurt's Space with Earth - alternate version of the hires space mod, but requires ADaoB posted directly above.
+Tacticool- Makes your rooty tooty point and shooty weapons purtier. 
+Cutscene Rebirth- Increases the resolution of the intro cutscene, where Goggles wakes up from cryo.

These mods don't really change the nature of the game - they try to keep it as true to original form as possible.

Enjoy!

Thank you very much to all the modders who spent their time improving and working with SS2. I very much appreciate it.