How to connect earthed metal chassis to DC ground?
Not a real answer, but it got too long for a comment.

There is not really enough information to give a really good answer. It may work OK with everything grounded to the case. EMC regulations are performance based. The FCC doesn't tell you how to ground things. It just tells you how much RF you are allowed to radiate into space. If  you have a bunch of stuff inside a metal chassis, and grounded to it, you have a good chance of passing radiated emissions just because your metal chassis will act as a Faraday cage.

But, the most important thing is that you MUST run a GND wire from board to board with every serial connection. So if the main board has an SPI interface connected to a peripheral mini-board, you must run a dedicated GND wire along with the other SPI wires. Preferably, the GND should be twisted with the SPI clock wire. If possible, it would be even better to run a GND wire along with every signal, and twist it with its signal wire. It is almost like you are wiring a differential pair, with the signal being one element of the pair, and the GND being the other element of the pair. This will greatly improve (reduce) radiated emissions, and also preserve signal integrity.

It doesn't sound like there is any major safety concern (as far as shock hazard goes). You just need to give some consideration to wires and fuses and short-circuits. You just don't want a wire to ignite a fire if it carries a large fault current as a result of a short-circuit somewhere. A few strategic fuses can probably take care of this.

The only shock hazard would be associated with how the AC power enters the box and how the chassis is grounded to the protective earth ground. I am not an expert on that stuff. I think you just need one solid, low-resistance connection from protective earth to the chassis. Sometimes a chassis will have a metal stud for this purpose.