Hi hi hi... You don't have to edit any original Q3 material to make your gun work in-game. You don't have to open any of the original .pk3 files, you just add your own and it over-writes the originals.
If you've edited any of the original Q3 .pk3s then copy and paste them from your Q3 CD and over-write whatever you've changed, because you don't need to do that and it might cause problems.
Check out http://www.polycount.com/ and download one or two of the weapons from there. See what they have in their .pk3s (note you don't have to call them pak9.pk3, call them my-weapon.pk3 or something). Do everything they've done, follow the naming conventions and add only what they've added.
Follow those conventions and you should be fine.
If it still refuses to work then check out the Polycount forums at http://dynamic.gamespy.com/~polycount/ubb/Ultimate.cgi and I'm sure those guys can get everything working for you