Det_Bullock: If you have the Logitech profile software you don't need the joy.com file or at least you shouldn't, that file essentially does a "calibration" of sorts at the start but in the end it only maps the speed preset keys to the throttle which should be possible to do with the Logitech software without doing the "throttle calibration" every time you start the game.
It's basically for those people that have joysticks without similar software, you can ignore it.
The profiler will allow you to map all the buttons and the throttle wheel/lever/slider, essentially you have to map the speed preset keys to it.
And yes, it should allow to map the hat and the buttons, also to remap the few buttons (up to 4) that the game recognizes.
For the graphics there aren't many tweaks I can think of, though perhaps you should set "aspect=true" to avoid stretching if it isn't already set that way, this being a 3d game scalers don't.
I just got a Logitech X3D (pretty much so I could play this game and a few other old favourites again) and have been able to get things setup mostly the way I want using the profiler, which is awesome, but the throttle is still a little off..
Do you know if there's any way to make the throttle behave like a single button press when it moves zones, rather than sending repeated commands (causing the full throttle *ding* to continuously go off) using the profiler?