Alright, so I've updated the wiring diagram with the following changes:
- simplified connections to the 6PST relay
- 6PST relay to be replaced with a contractor driven by a relay. Just didn't want to break all the connections and rewire everything
- 24V and 5V PSUs
- 12V fans wired in series to the 24V PSU
- limit switches moved input pin
- home switches wired in series, with override switch and 5V idiot-proof buzzzzzzzzzer
- two input pins left, most likely one of which for a touch probe to come in the next few months
Click image for larger version. 

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I've also updated my original post with the answers to my questions and the new diagrams, so that anyone coming in the thread can follow along without reading through all messages.