Don't use y axis. Delete that option.
Use Mouse forward/backwards.
It's an option under Controler Setup/Advanced/Mouse.
I found a better way to set it up. If you do what you stated to do, the game uses the digital controls. It does work, but aiming up/down is kind of slow (at least for me it was). What i did was i changed "Mouse Y Axis" to "Analog Moving". Then in game just turn on "Mouse Aim" and it should be set up just like a modern day FPS. The up/down is a lot smoother and faster in the analog mode than it is with the digital setup. Although aiming up and down sort of distorts the graphics due to a lack of perspective correction. But it will do that with the digital setup as well.
Hope that helps you little bit. That's how i play it at least. It took me a little while to get a good configuration. (Also even though it is changed to "Analog Moving", it won't move you forward/back with the mouse if you have "Mouse Aiming" turned on)