I'm not terribly familiar with the M916A1 charging system, but I would start by looking into the electrical troubleshooting section of the unit maintenance technical manual. (TM 9-2320-363-20-1) The electrical troubleshooting section starts on page 3-11 and shows the following sections -
ELECTRICAL SYSTEM
CHARGING CIRCUITS
1. LOW BATTERY VOLTAGE
2. BATTERIES NOT CHARGING (EITHER VOLTAGE), VOLTMETER INDICATES VOLTAGE
3. BATTERIES NOT CHARGING, VOLTMETER DOES NOT INDICATE VOLTAGE
4. +12 VDC CIRCUITS NOT CHARGING, +24 VDC CIRCUITS NORMAL
5. +24 VDC CIRCUITS NOT CHARGING, +12 VDC CIRCUITS NORMAL
I would suspect you may be able to find out some information in there. The manuals for these trucks contain information for the M915A2, M916A2, and M917A2 as well as your M916A1, so be sure you're looking at the correct information.
I think artisan has some electrical system diagrams for the 916s in his build thread.
Artisan's thread is good, but it has info about the AM General M916, not the Freightliner M916A1, which is significantly different in the electrical/charging system department.