Hi Andy,
I have a similar situation so I just jumped in on this thread.
Been wiring the 6i25+7i85S boards for an XYZ mill project but can't seem to make it work. We're still using a Universal PWM from Pico.
I used only XYZ PWM, DIR and XYZ A, B & I encoder signals. That leaves me extra I/Os.
I flashed the boards using the 5i25_7i85SPX2.bit.
This caught my eye: "Note that there are 17 perfectly usable 5V TTL GPIO pins on the second header of the 5i25, though."
Are you referring to the I/O connector 2 on PNCCONF, the same as this 2nd header of 5i25/6i25? And the I/O connector 3 (on PNCCONF), the 25-pin going to the 7i85S?
Hope you can clear this out for me. Thanks. Nuki.