1994 Dodge Spirit Code 41

Code 41 came up after the check engine and gage lights came on. Checked alternator, needed replaced, so I got a good one from scrap yard. Checked OK. Put it in and still Code 41 with check engine light still on, sometimes it will go out. Gage light will clear when battery charger is put on and charge cage goes up when I charge the battery. Afraid to drive as it may stop on the road. Can anyone help what else the problem might be and Code 41 goes out and the system is working fine. Thanks
Doug