I think I have it fixed. I ended up buying a 4 foot long 6 gauge wire (probably overkill) and crimped on some heavy terminals. Went straight from Alternator out to Battery positive terminal.
Before starting I measured 13.2 V on Battery (I had it on the charger all night). After wire hook up and starting I measured an appropriate 14.something volts on battery.
I then took it to the auto parts store for a charging system test. Everything tested just fine. Battery is great. Alternator and Voltage Reg is just fine. All this trouble for old wires. Live and learn. I wouldn't have had to buy the last battery and alternator 9 months ago had I known what I know now.
Thanks for all your help guys.
I'll know for sure when I give it the 500 mile drive to work routine next week. But I suspect every thing is cool.
P.S. now my radiator is leaking...
oh well it never ends. I'm ready to tackle this next project. It will be a cake walk compared to the heater core replacement. I think I'll try some stop leak first.