Good advice. After speaking with a Lucas Arts tech rep today, he informed me that the best thing to do was make a copy and use the copy to run the dedicated server. Right from the words of the tech. He also stated, that while those using illegal copies will get kicked (teaches those that buying games and supporting them leads to better games in the future) is normal.
As for the ports, those listed on the Lucas Arts page may be incorrect as they state the JK2 ports are in the 28k range. JK3 runs off of the 29k range. The page states JK3 are in the 28k range.
I will forward those ports stated and hopefully that will work with UDP only. I agree that I only use the dedicate PC for hosting games so opening up a 1000 ports is no problem, but it doesn't mean it's a good idea in the end.
Thanks for the advice man!
BTW - The tech support stated that he was going to look into the problem that I had and email with any information he can find out. He did state, however, that since the game is so new and the "leaked" version is out there, everyone with legit copies are suffering for their cheap actions.