I download the mod, copy the files into the Cortex Command folder, with all the other .rte files, and when the loading screen comes up, where it goes through all the files it says it couldn't match and has to abort. Can someone please help me fix this? It has happened to all mods, and I have build 27 if that helps.

Well, most of the mods are now using CC version 1.0 now instead of the former builds.
Thus many mods are referencing things that are in different places then they were before.
This of course leads to errors since the mod can't find the files in question.

Recommendation: Post error message screenshot AFTER installing cc 1.0

How do I tell which version it is? I did not buy it on steam, it is an .exe file

Get an update to 1.0 CC.

Kinda confused how you told me you're using Build 27 and then proceed to tell me that you need help figuring out what version you have?

Build 27 updates into version 1.0

You need to go to wherever you bought cc and it should have the new installer.

Its all good I have a different build which allows me to mod, thanks!