how did you wire up an electric fan with no relay?
with 20 year old wiring, you could have a decent voltage drop through that stock wiring and switches, to the headlights. i installed relays on lows, highs and fogs to help with this situation (gets battery power to the lights rather than using the recursive stock wiring).
and it sounds like either you have a voltage drop in the wiring or an inaccurate gauge (dont 86's have an ammeter rather than a voltmeter?). straight up on an ammeter gauge would be around 12.6 volts.
good luck.