Master shut off switch charging problem

Im not sure if this is the best section for this question, but it’s race car related. I have a ‘71 Duster D/SA Nhra legal stocker. I just install a second battery in the trunk, per Nhra rules we must run a battery in the stock location also. So I have one up front and one in the trunk. Both are Group 26, nice they only weigh 28#.
So to get the car to shut down with the master switch you need to kill both batteries and the alternator. I found that if I interrupt the wire that runs from the amp gauge to the starter relay and disconnect the positive terminals the car will shut off. Wiring is mostly stock, I still use a key to start it. I ran the two positive battery cables to one side of the master switch, and the wire from the amp gauge also to the same side of the switch. Then one battery cable back to the starter and a jumper to the starter relay. I used #1 stereo amplifier cable for the batteries and #8 amplifier cable for the alternator wire. It was free seems like good stuff? The car runs and does shut off with the master switch, but still has some power, I know I can fix that by going to a 4 pole switch, I’m messing with an old 2 pole now.
The problem I’m having is the alternator is putting out 14.6 volts but I am only seeing 12.6 at the batteries when running and 12.4 or so when not running. It’s a power master 50 amp alt. The alt wire has 14.6 at the master switch.
What am I missing here?