I've tried reading all the documentation (most of which is apparently marked as outdated, and there isn't an up-to-date guide), and I can't figure out how to enable and disable shunt mode / ATC mode at all.
Shunt mode won't go away, and ATC mode doesn't disappear after you do shift + up arrow.
Does anyone know how to enable and disable shunt mode to remove the speed restriction, and enable and disable ATC mode please?
Shunt mode is a feature of the interlocking system. It only gets enabled when the train is in a track section (you have TCBs set up) and you switch the driving direction. The purpose is that in real life, when doing shunting, you are only allowed to go at a certain maximum speed.
When in shunt mode, the train obeys dwarf signals (shunting signals) and stops at them when they're red.
To switch the train out of shunt mode, you just need to pass a green signal (main signal) with it. Then the train knows that the path ahead of it is clear and it can go to the full speed again. If you do not have a green signal at hand, you can also use the sign with the green arrow and S on it (remember to set the influence point).
If you do not want the train to switch to shunt mode, then remove all track sections and TCBs in the area where you are.
The ATC indicator just means that the train is holding a speed set by an ATC command (or by pressing the Shift+direction key combo). This can be cleared at any time by pressing Space (or whatever the Jump button is - the same button as for braking the train). This will also stop all pending ATC commands the train may be executing.