Kit V2 use the All In One board. Look here for Kicad design files and the schematic in svg format.
All the Zynthian kit versions share the same specification:
The use of a GPIO multiplexer (MCP23017 or MCP23008 for super early versions) for the encoders and extra switches. These components use the I2C protocol on RBPI BCM pins 2 and 3 (SDA1, SCL1). This is not an issue in your case because an I2C line can handle multiple devices. It use also two other GPIOs but these could be any of the free left GPIOs.
MIDI is handled through the serial line (UART) on RBPI BCM pins 15 and 14. RX for receiving data and TX for sending. This could be an issue for you. I don’t know what usage the Argon case make of BCM pin 14 …
If your USB interface has MIDI conections, you can use them in Zynthian.