Has anybody been able to make this work properly with an XBox 360 controller? I can get certain buttons and the left analogue stick to work but not much else.

My guess is it's too old to support the second stick and such. Other older games have problems too. I suggest getting xpadder or a similar program and setting a profile to make the right stick correspond to a set of buttons, while leaving the rest inputs blank (so that they function the same as now). You could make the right stick be like the arrow keys, and set the arrow keys in game to do the strafing functions or similar functions, anything that doesn't need analog control basically, leave those to the left stick). If other buttons don't work either, set them as keys also, to the functions you want. I did this for Tachyon: The Fringe and FreeSpace 2.