I am having trouble getting used to the rather clunky controls and I was wondering if any of you have any recommendations as to what I should do to that would help make the game controls work with me rather than against me. Any assistance will be very much appreciated!

I had some trouble as well; the keyboard controls are a bit oversensitive with how your ship kind of "snaps" between states as you turn, and the mouse isn't "Drag to steer" like I'm used to, but basically a joystick.

If you have a game controller of some sort (Like an XBox 360 controller, a Dualshock 3, etc.) I'd suggest trying to calibrate that. I've used a Dualshock 2 with USB converter on my computer for quite a while, and it's great for most games. Although personally I just stuck with the keyboard.

EDIT: From a joystick topic, a custom version of DOSBox with support for setting the deadzone on a joystick.