What you're trying to do isn't feasible with python.
What you want to do is essentially make a new driver for your mouse/keyboard.
This is not system independent and there's no good/nice way of doing this with python.
PyUserInput attempts to abstract out the system dependency - but this is not complete, and it cannot override the keyboard/mouse completely. What it can do is it can mimic actions on your mouse or keyboard only if the application allows emulated actions. A lot of programs like games and a bunch of other software disable emulated actions.
The most stable and significant tool which is not a driver level tool are autoit and autohotkey - you could try making an autoit/autohotkey script which is executed as a python subprocess and use pipes to send and get info from the script.