Standard linear voltage regulators typically have full output short-circuit protection built-in - just use a separate one for each part of the circuit, and then think about the consequences of some parts being powered down and others powered up (if its just sensors that get shorted, typically nothing bad happens, but if an output valve has lost power you might be feeding a logic signal down a wire to a short circuit - adding 1k resistors in series with such signals can protect output pins.
You might also want a few voltage dividers to monitor various power rails so your code can detect damage.