Yeah, I shouldn't have included a models.dat in JKE to prevent these sorts of issues... sigh.
What you need to do is make sure none of the files have the same name as anything in JKE.
Rename the 3do file to something like Duke.3do
Rename the textures. say, Duke.mat. Open the 3do in notepad, and make sure the texture names there are the same.
Open the models.dat from JK. Update the model count at the top by 1, and add your new model to the list at the bottom.
Pack the 3do, textures, and models.dat into a gob.
Test it in normal JK. It should work, you should be able to select the model in MP.
Test it with JKE enabled. This is where it gets tricky. the way JK loads gobs is dependent on your operating system. Mine loads them alphabetically. Your gob has to be loaded after JKE, to make sure it uses your models.dat. I would just name the gob something like ZZZ.gob to test it.