Pls note that Nanaki's Fleetmod and Motherships Mod from Goblin_Wizard are both in the Mod itself. No need to Download it through the Merged Version, its only for people that just want to play with these two Mods.
It also would Break some additional Stuff when you Install it with the SW3.Expansion Mod.
-About the Problem:
Oh, seems to be only an Invalid string the Modules.xml File, I get right to it. Will post Quick fix when its done.
EDIT: Fix
Modules.xml
Also: Be sure to read that readme.txt