Hi Andrew,
Yes, you have to use the RJ45 axis connectors to connect the step and dir signals to the drives, there is no duplication of them on the screw terminals, they are only in the RJ45s.
You can get a patch cable and cut off the RJ45 plug from one end and connect the wires how I described.
You can get patch cables easily, because they are used to connect internet, so basicly every IT and electric multi store has it.
You can find a picture of how this connection looks in real life in this forum thread:
download/file.php?id=578&mode=viewUnfortunately I could not find a more closeup picture at the moment.
The issue with general drawings is that there can be lots of possible configuration, because you know all I/Os in the UCCNC are freely configurable,
so you can configure limit and home switches to any of the inputs and you can configure an e-stop to any of the inputs, you just have to configure the port/pin number according to your connections.
What are in the manual are connection diagrams of different sensors, like PNP, NPN, machanical switch which drawings basicly covers all possible connections.
And making a concrete drawing could make the customers think that I/Os on the board are fixed and so they could easily and falesly think that they can't use the board with their controller if it has another pinout fixed configuration in their controller manual. (E.g. like in some chinese motion controllers.)
What we could extend and probably we should in the manual is how to connect the step/dirs to the drives.