Welcome to the forum. Unfortunately, you have posted to the Premiere (no Pro) forum, and you want the PrPro CS4 forum. Maybe the MOD's will move this to the correct forum for you.
In the meantime, lets see what we can do to help you.
First, the .MOD files (I assume you are shooting with a JVC) are problematic. This ARTICLE will probably help you a bit. Follow the links.
Next, in the PrPro forum, you might want to Search for "MOD" and read some of the articles. I've been involved in some of these, so you should be able to filter on "the_wine_snob," and get many of these. There are some good discussions and also more links. Also, Ann Bens has been involved in many of these, so a filter on her should help too.
2. When I export video and encode it.. all settings are proper and I can not get audio on the final file... thoughrts???
For this one, you will have to fill in some blanks, as to the full and exact Export settings used, plus some background on the Audio portion of your Timeline.
3. I have a pinnacle box with a firewire, composite and s-video inputs and outputs... Pinnacles own software recognizes it as a source, Adobe Ultra likes it, but I can not get Premeire to recognize it as a source. THoughts????
I doubt that Pr will see the Pinnacle A-D bridge. Again, you might want to do a Search of this forum for "Pinnacle," and filter on John T. Smith. He has posted to many threads, regarding Pinnacle A-D setups, and knows his stuff.
Sorry that I cannot be of more direct help to you, but hope that I have given you some things that might get you closer to your desired end.
Here is a FAQ entry, that might have some info on the JVC footage/files. Sorry that the screen-cap is now dead, since the forum changeover. It was written for PrElements, but some might help you in PrPro.
I will persue those avenues...
thanks so much.
1. Don't use those cameras. Use only tape based MiniDV models.
2. This may well resolve after implementing the fix from # 1 above.
3. Remove this entirely, it's unneeded. MiniDV cameras connect via Firewire.