So it seems you did everything right, but one more question remains unanswered: what folders do you have in Conquests/Scenarios? Apart from other mods you may have, do you have any other mysterious folders (should be WH-Mod only). I ask because you could have extracted something to it's own folder.. if you're sure you didn't, ignore it.
This is quite unexpected, I don't think anyone had this problem before. There are even no "SS_Thrusters" in the mod... Such things sometimes happen to me with mods ie. if I run out of resources (running civ3, photoshop, poser, several websites, winamp...). Can you open WH-Mod.biq in the editor, run through all Improvements and Wonders and see if BLDG_SS_Thrusters appear in Civilopedia Entry box?