This requires some planning out.

Once I have mounted the Pi's to the pedalboard I need to measure the space left for the enclosure:

Length: _______mm

Width:   _______mm

This will determine the amount of buttons and functions I can fit into the box.

Reaper Pi - essential controls:

Channel selection (two buttons? Or an encoder?)

Arm track to record (button)

Record / Stop (button) 

Desirable: mute/solo/undo buttons. Could be added as held button press features.

Pisound - essential controls:

Pedalboard up/down (two buttons)

3-4 effect switches (with LED feedback to show on/off)

Analog inputs broken out to trs jack's for adding expression pedals.

I2c breaking out for possible extension button boxes to be added.

Research to be done:

Gut instinct is to run two Arduino Pro Micros as co-processors for this to give two native USB ports out. One used as a usb midi input for the Pisound, and the other as a usb midi device for shortcuts in Reaper.

I've picked up a Raspberry Pi Pico recently, and running Circuitpython on that also allows for native USB use. They're really cheap, so may also make for good choices for this.

Other options: run a software serial port out to a hardware midi jack and send midi data to the Pisound via the midi jack, dropping the need for dual controllers.

If there's going to be a network established between the two Raspberry Pi boards there's a shout for using an ESP8266/ESP32 board to send wireless MIDI, perhaps. 

There's even a shout to use a Pi Zero in USB ethernet gadget mode to share one of the Pi's network connection.