If you're going to start doing that then you're probably taking this beyond what the OP originally intended. If you want to control with MPF, you might want to take a look at LISY. That replaces the MPU board in your machine, can run the standard game code (it has pinmame embedded to do the control) and can also be connected to a computer running MPF. In that case it basically becomes a "slave" to MPF.

https://www.lisy.dev/lisy35.html

But I love what the OP is doing with this, hooking an Arduino to the board and trying to get it integrated with all the existing components is really clever

The Teensy 3.6 has been my goto-board lately. Nice and fast (180Mhz), no funny Neo-Pixels, onboard SD card slot, lots of memory and I/O, programs easily from the Arduino IDE.

https://www.sparkfun.com/products/14057#features-tab

There is also a 4.0 board with processor running at 600Mhz but that's faster than I need....