The alternator needs the battery in the system to regulate charge voltage. I would do an error code check on the ECU and see if anything comes up. Vehicles in the 90's began to have active charging regulation triggered by the ECU. I don't know if the MM fits into this category though. The biggest gremlin in an electrical system is a bad connection somewhere - usually the grounds get funky and no longer have a solid connection but you've stated that you have cleaned them all so that is a good start.