For the Matias buttons, what happens if you connect firstly from the Core J89 to the second board etc.? How does it look if you disconnect the boards in turn, starting from neo_85?
Check the soldering around Core J89 and IC3. Maybe the data signals never leave/enter the board?
How do the ICs look on neo_ boards? Any pins bridged? All diodes with the correct orientation?
Axes board IC1 could be nicer, but if it works probably leave it as is. For the LED, is it the proper bipolar type? Does it light up with a multimeter diode test? It should light up in two different colours depending on the orientation.