Basically, this is their Piston Twin Quadrant http://www.flyelite.com/hardware.php?product_id=18 which is normally used for flying twin's like the Baron. (2-Throttles, 2-Props, 2-Mixtures w/o any detents. They also sell a King Air PQ but I'm not to that point yet. Let's see if we can figure out the Twin PQ first.)
If I understand your documentation correctly, I should find a FS9.cfg file "somewhere" in the FS2004 directory structure that lists all the known Joysticks. However, I don't seem to find one anywhere. There's a FS2000.cfg file but that's it. (Maybe I should just completely remove FS2004 and reinstall it and FSUIPC along with the Elite driver and start over.)
Also, if I look at the normal FS2004 Controls->Assignments page, all I see for joysticks are the CH Products USB Pro Yoke and USB Rudder pedals (i.e. FS doesn't even seem to see the Elite levers as Joysticks at all).
FWIW, Elite has a completely separate menu in FS2004 that you are supposed to use to calibrate the levers on the PQ. However, I've yet to be able to find a setting (or offset + setting) that results in the props going into the Feather position on the Power Console window. It's as if FS doesn't even see the PQ at all but yet the Elite PQ "does" operate Throttles, Props and Mixtures normally with the exception of going into Feather.
Finally, if we can't figure this out together, would you be open to a 3-way call with you, me and a key development engineer at Elite to get you guys talking and working together? I'm trying to get through to the CEO of Elite to get something moving. Their TechSupport doesn't really seem to know anything.