Remaining blocker
Net rename collisions prevented applying the complete pinout (e.g., multiple intended pins wanted to become GND, +24V, and DI_Y_LIM, but those net names already exist, so Flux rejected the renames). Until I resolve the connector pin labeling without colliding (either by keeping per-pin nets like J2_2/J2_4 and explicitly connecting them to existing GND/+24V nets, or by using unique net names like GND_AO/GND_AI and then tying to GND), I cannot accurately finish the remaining wiring and documentation.
Next steps
I can finish this in the next pass by:
Rewiring J2/J3 pins to the already-existing GND, +24V, and DI_Y_LIM nets using rewrite_connections (no renames required).
Completing analog IO wiring (DAC -> U21/U22 -> AO_X_CMD/AO_R_CMD, ADC inputs -> AI_Y1_SCALE/AI_Y2_SCALE), three LVDT channels (U13-U15), ISO1211 input conditioning (U23-U32), and valve drivers (U18-U20 with Q1-Q6 and D1-D6).
Then normalizing metadata with rewrite_component_properties, re-checking ERC/DRC, and exporting Gerber/ODB++/BOM/pickplace/STEP.