I'm now convinced you have extracted the mods correctly and have them in a mods folder. I'm not sure I understand which mod folder.
I get the impression you have two folders for the game in your My Games directory, one named GalCiv3 and the other GC3Crusade.
Since you are trying to use mods for the Crusade expansion, I have to assume you have that expansion and maybe more.
Which version of the game do you have? The main title/menu screen will tell you.
If you do have Crusade or Intrigue or Retribution or more than one of them, you need to be using the Mods directory in Documents\My Games\GC3Crusade for all your mods. The game will ignore the GalCiv3 directory if the GC3Crusade directory exists.
It's possible that some of the mods you want to use won't work correctly with the version of the game you have and cause strange results during a game, so keep that in mind.
Until we get mods working, you should ignore the prefs.ini file. Use the Options menu in the game to turn mods on or off. The ResetPprefs=0 is correct and shouldn't be changed.
Finally, I don't think 77 is all that old. I'm 72, and most of the time I don't think I'm old.