WHOA, this is awesome,. Are you concerned that there will be too many wires attached to a single housing/enclosure?
Very nice work. Cant wait to see this in action.
No, it's great to have a physical device in front of me, that helps me to think how to proceed, both in terms of software and housing.
A solution for the 2.5mm plug I've found already, so I'm not going to change that.
Just as a BRAINSTORMING exercise, this is my thought so far:
From a housing point of view, put the PCBA's on their USB/NIC as bottom, try to avoid moving salt water to go 'upstair'. Technically we can avoid any connections from the upper part shown when turned left. Presently salt water is my biggest concern. Ideally some over-pressure from the outside (living room) into the top of the housing could be ideal, both for cooling and keeping salt away.
Electronically, change the Reef-PI_HAT into just a power supply and 16 channel digital IO board. Then no power supply directly to the Raspberry PI would be required (as you are using) and moving any connections away from the top side of the shown picture (which would be on the left side when turned as proposed). Yes the Reef-PI_PWM module has connections there, but who needs more then 8 PWM connections and ultimately it would be possible to use 2 Reef-PI_PWM modules;)
From software point of view move ATO and Dosing Pumps to separate boards like the Reef-PI_PWM with an MCP23017 (I2C), Then basically we're unlimited. (not sure about ATO interface at the moment, analog?)
PH/BNC boards would also be possible.
Back to housing, if we can agree on a sequential range of boards (e.g. PI, HAT, PWM, PWM2, BNC, ATO, Dosing,....), people could install the boards which they require, while 'over jumping' missing boards with just a 6 pin connector. All output connectors could then be on the same housing in a different configuration.
Again, this is just a brainstorming in coming to a flexible but compact and rigid solution involving Software, Electronics and Housing. :D