Unzip this mod and you'll get a .pak file - just drop that file into the Paks directory (find where System Shock is installed, then go into SystemShock\Content\Paks). You should see the game's main content .pak, which is called SystemShock-Windows.pak, in that directory. You won't be replacing anything.
Also, be sure to remove and/or update outdated mods as game updates come out. Sometimes game updates will not affect some mods in any way though, so if your game doesn't crash with older mods, you should be okay depending on what they do. Music mods, for example, haven't been affected since the game came out.
do you have something overwriting this like an older ironman version (1.2 or older; 1.3 has this built in)? try renaming this to zDynamicRapierColor_P.pak or if that doesn't work, SystemShock-Windows_zzDynamicRapierColor_P.pak to try to push the priority higher than other mods.
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Also, be sure to remove and/or update outdated mods as game updates come out. Sometimes game updates will not affect some mods in any way though, so if your game doesn't crash with older mods, you should be okay depending on what they do. Music mods, for example, haven't been affected since the game came out.
Still have no idea how you got this to work but its super fun. Cheers!