might be worth noting down wiring as it is and then starting again.
Excellent idea.
Is there any way of checking where wires go when they enter the wall behind the junction box, or just by removing the room stat downstairs etc to see what wires are what.
How many cables go into the wall and where do you think they go?
Don't forget all the wires in a cable must go to the same place. So you only have to identify one wire in a cable and the others are obvious.
Non standard colors are a great help (i.e not brown, blue or green/yellow)
If you have a multimeter you can use that to identify cables -
with the power off. For example, turn the room stat to max. Find what you think is the other end of the cable to the room stat and disconnect it. Set the meter to Ohms or Continuity and connect the two wires to the meter leads (either way round); Depending on the meter it will either beep or show a very low reading. If this happens, you have correctly identified the cable. You can confirm by setting the room stat to min, the meter should stop beeping or go to open circuit. If no result, try another cable with the same colours. In some cases you will have to disconnect the wires at one end and temporarily twist them to gether to make a circuit.
The terminal box in the original pic has 8 connectors, dont know if that makes any difference.
I take it you are talking about the terminal box on the wall. If it is just a strip of 8 connectors, it can be used. This is the the "junction box" in the Apollo wiring diagram.
The diagram shows the pump connected directly to the boiler. As your pump is remote you will have to connect it via the Junction box. Connect pump Live to a spare terminal and run a wire from that terminal to the boiler pump live terminal.
The diagram shows the neutral connection coming from the boiler. Is that what happens in your case or does the neutral come from somewhere else?
I assume the Main power connection is direct to the boiler,as in the diagram.