I was replacing the Fan control module and in the process removed the battery box to gain access to complete the installation. During the installation process I noticed a two wire connector tucked under the battery box. Would anyone have any suggestions as to where it belongs or is it for an option that I don't have on my car.

 

The connector was for the battery tender when the car was shipped there is a stub on the bottom of the battery box that the connector can be plugged into. It is possible that it has been broken off of your battery box, but check for it. It is just a holder so the connector isn't flopping around.
My battery box has the bracket intact and the connector is plugged into it.

 

I expect it will be for the transit relay used during shipping from the factory.

There are pics here https://www.jaguarforums.com/forum/x...esolved-81368/