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When I tried to install the game the installer told me that it was skipping all the files. To fix this I created a folder on the root of my C: drive called T3Mod. So it was C:\T3Mod. I then created all of the necessary folders for the files that were being skipped inside the T3Mod folder. I got the names and locations of these folders from the same place in the installer that tells you it's skipping files. I then placed the installer in the T3Mod folder and ran it there. All files then extracted properly. Then I moved the T3Mod folder to my steam\steamapps\SourceMods folder and then restarted steam. The mod then worked from there on out.
It appears that there is a problem with the nullsoft installer, that sould really be addressed by the creators of the mod. The installer doesn't seem to want to create new folders so it just skips all files that don't have their folder already created. It also doesn't seem to automatically find the folder where you have steam installed.
I should add that I had no problems with "The Way" mod. Hope that helps in solving the bug.