I'm not sure what you're after, but the mouse axises are properly set up by default, you just need to change the button configurations (if you want), go in game and press U.
OK, well, I obviously messed up the configuration somehow because even though I deleted DUKE3D.CFG, the game still registers my last incorrect efforts to map mouse Y-axis.
Are you sure you know the problem I'm talking about? I feel you are operating from a perfectly normal config and and assume I am too, which is not the case... I am trying to illustrate from the attached screencap that I cannot map vertical look to mouse Y-axis.
CORRECTION: there is no option to assign ANALOG vertical look to mouse Y-axis. However, as a temporary measure I have assigned DIGITAL vertical look to mouse Y-axis. I gotta tell ya, that's not so hot. when you're used to analog... :-)