I think I'm getting closer. I downloaded a controlmap file from http://www.skyrimnexus.com/downloads/file.php?id=246, and I've determined that the keycode for the joystick axis is 0x000b however the game still goes to controller only mode when I have an xinput.dll loading.
So far I've added 0x000b to my controlmap.txt in my skyrim\Data\Interface\Controls\PC\ now I just need to figure out a way to disable controller only mode.
I have been trying to accomplish joint 360 Controller and Mouse/keyboard input in the controlmap.txt file since release day of this game and from what I can see, it is just not possible.
As soon as you enable Xbox 360 support in the Options Menu (which you have to in order to enable anologue movement on the left thumbstick), all mouse input and the
majority of keyboard input (exceptions include the Quick Save/Quickload keys and the console key) is automatically disabled by the game engine and I remember that the two
Fallout games had the same problem.
I like to play using the mouse in my right hand for turning/aiming and attacking, etc - and the controller in my right hand for basically everything else. I do have Pinnacle Game Profiler which is a fantastic program, but unfortunately it can only emulate anologue xinput on the thumbstick if you have enabled controller input in-game, which brings us back to square one ...
I think the automatic disabling of one type of input, if the other type is enabled, is hard coded and unfortunately could only ever be changed by the developer (which I predict they will never do).

Stannie