Yes, the infrared goggles aren't in DFMod because Jedi Academy doesn't have them.
Make sure you're starting the mod from a separate desktop icon shortcut, NOT from the Mods menu in the regular JA game. That has been known to cause various issues. If that's not the case, uninstall any other mods, update Jedi Academy to the latest available patch, and then try running DFMod (using the desktop shortcut).
If that's not the case, you may have downloaded a corrupted file. There shouldn't be anything wrong with the files on the server but sometimes things don't download properly or get "damaged" during download.