I changed my mind, I think the programmer should be able to be reprogramed without any special tools.  This means that the Microchip processor is getting removed and replaced with a USB to serial bridge.  I have decided on the Silicon Labs CP2104 USB to serial bridge. My decision is based on cost and minimal external components. I went to several suppliers and compared 1K quantity prices.  I also confirmed that I can used the built in USB VID and PID.

I followed the example circuit in the datasheet for the CP2104 making minimal connections for a self powered device.  Since I am going to eventually have a battery that is the correct mode to wire for.

Since I no longer have the Microchip processor to control the high voltage, I connected the SET line of the AAT1230 to GPIO15 of the ESP12E.  The pulldown on GPIO15 will keep the voltage regulator disabled during a reset and I will drive it low anytime I am not using it, minimizing the current it draws from the battery.

I connected the Feedback voltage from the high voltage and the target voltage divider into an analog SPDT switch(NC7SB3157 chip) and connected the common terminal to the ADC input of the ESP-12E.  This allows me to verify what voltage the target system is at and what Vpp voltage is maintained during programming.  I ran out of IO pins on the ESP-12E, so I am added an SPI port expander(MCP23S08).  I have to give up 1 pin for chip select but I gain 8 general purpose IO pins.  So I moved the data direction control pins to the port expander and then connect GPIO5 to the CS line of the port expander. I verified the port expander could operate at 3.3V to match my operating voltage.

I connected GPIO2 to the Switch select line of the analog switch.  A high selects the VPP voltage divider, a low selects the Target voltage divider.  The voltage dividers are necessary because I could be dealing with more than the 3.3 V that the ESP-12E can handle.

None of the new devices were in the libraries.  I had to create each of the MCP23S08, the CP2104, and the NC7SB3157 in the schematic library.  I still have to connect the Vpp line to the target connector where I can leave it high impedance, set it to high Voltage, or Ground it.