Rcimp,
Yes, you can get rid of all the mess! Any alternator version you choose will have the large gauge BATT wire. With the single wire unit, that's it! With the three wire unit, there are two more wires..the ones utilizing the DA plug. If you wrap #2 around at the alternator, the only wire left to deal with is the small #1 'excitation' wire.
You can make the connection from alternator BATT to the existing BAT wire on the voltage regulator on the firewall. If this wiring is intact and proper, this should route power through the ammeter and to the battery.
The #1 wire needs to see voltage when the truck is running. I don't know what you had before, or what worked before, so all I will say is that you need to connect this #1 wire to some other wire that springs to life when you turn the key to ON.
This rig has already been converted to 12 volts in all the other areas, correct...coil, lamps, gauges etc. Keep at it!
Stuart