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Apologies for all the replies, I keep forgetting to add important bits of info. This should be the last of it though.

The 3 limit and 1 EMO/Estop inputs (pins 1-4 on the DIN, and 5 if you want the...

Forgot to add these ones as well, which shows which connection is which on the parallel port. The first image has all the pin mappings excluding the 4th axis and emergency stop. The second image...

Just posting this here for others, but I found someone who had a physical copy of the manual for the MicroProto. I was able to get them to send me images of the I/O port documentation:

Any updates on this? I'm in a similar position; haven't had any luck in finding these pinouts!