Hello F
I have been trying to hook up my alternator for a while now. The connector plug was missing coming out of the wiring harness, so I am not sure which wire goes where. If you get a chance check out my post under "still trying to hook up my alternator in 86 Trooper TD (more pics)". I have some good pics of the color of the wire. in your post you said

Chassis/Alternator connector
Black-white/Black-white ... Ignition (might be black-yellow since it's very dirty)
White/White ... 12 V battery
White-Green/White-Red ... measures 86 ohms - charge relay

but my alternator wires are all white. So I was thinking on my trooper it would be

Chassis/Alternator connector
Black-yellow/White-blue ... Ignition
White/White ... 12 V battery
White-red/White-Green... measures 86 ohms - charge relay

Any Ideas
Thanks
Billy