There is no option to change resolution. You'll have to adjust your Windows desktop resolution to a lower setting before playing.
Joystick and pad controls are made to Xbox controller specification and cannot be adjusted (supporting non standard axises would be too much works vs benefits). I have tested an original Atari/Commodore 2-axis joystick with an USB adapter - and it worked well. But this also might depend on the axis mapping of the USB adapter, whether it works or not.
I might do a x4 zoom option for 4K. (Current implementation is x2 the original - and it works well up to 2K resolutions).
Added Zoom options for better high resolution support
A - automatic zoom when vertical pixels > 1300 (default)
x2 - always x2 zoom
x1 - always x1 zoom
Also OldSkool mode in windowed mode is never x2
Enjoy :-)
