Oh boy problems...

Another thing to check is the main power supply wire where it comes through the bulkhead connector. It's quite common for this connection to be burned or loose inside the connector itself, and it will give the symptoms you just described. Sometimes just getting out of the car, or moving around inside will cause the connection to loose power then for no apparent reason it'll fire up again. Also, are you still using the stock Ammeter in the dash? They can be a real head scratching pain in the a$$ and cause all kinds of electrical gremlins.