I spent a good amount of time last weekend hammering away on both cameras and testing settings. What I determined was that the one body I have over exposes by 1/3 of a stop. Using Thom Hogan's guide, I reset my correctly functioning camera to his recommended settings. Then I tweaked them to my liking. I backed up those settings to a CF ard and loaded them onto the camera I'm having trouble with. Both cameras are not set to match eachother exactly. Finally, on the bad camera I used custom menu B6 and set it to under expose by 1/3 on each of the 3 metering modes. This appears to have fixed the issue. Both the cameras expose dead on with matching lenses and photos now. Ultimately, that's what I was looking for.
Thanks to everyone for the help!
"Sometimes I do get to places just when God's ready to have somebody click the shutter." -Ansel Adams