With 3 different systems affected, I would start with the main connector at the PCM. All 3 of those systems come together there. Check to make sure the connector is fully seated and latched. If that checks out, remove the PCM and the connector. Inspect for obvious damage to the PCM socket and the connector. Clean the contacts on both with something like DeoxIT cleaner. DeoxIT also makes a preservative to protect the clean contacts. Make sure to completely reinstall the PCM before reconnecting the batteries and testing the system.