The M350 is TINY.
I use them with atom-based setups at work. For my application, they're great.
However, I don't know if the additional cooling needed for your Athlon II CPU would fit vertically within the case. Look for the lowest-profile cooler you can, preferrably something designed for a 1U server chassis.
If you find something, that will make it fit in the M350, but will also reduce the cooling capacity of your CPU cooler. That could present problems on a very hot day, when temperatures will rise substantially over ambient outdoor temperatures.
You're definitely not getting 3 physical hard drives in that case.
You can get a mounting plate for a second, but both hard drives need to be 2.5" drives. If you have the second HDD mounted, you have even less room for a CPU cooler.
Also, the M350 has no space whatsoever for a DC-DC PSU, save for the mini units that fit into the ATX power onnector (like the M3 or PicoPSU, neither of which are suitable for your hardware). It will have to be outside the case. I suggest putting it into a plastic project box, and running the ATX wiring to the M350 case. Considering there is no accommodation for the ATX power connector to come in from outside the case, you'll have to get creative.
You could use the space for a 40mm fan on the front, possibly, but you'll need to cut away some of the plastic bezel on the front.
Personally, I am leery of the M4, but others have had good experiences with it. I think it will suit your needs.
Remember that AMD's architecture draws CPU power from the 5V rail, so you need to make sure that whatever PSU you choose has sufficient output on 5v rail for your PSU selection, as well as the large number of USB devices you want connected.
Some of those USB devices you'll want connected directly to the motherboard (instead of to a hub, powered or otherwise). That will mean more draw on the 5v rail.
All of this needs to be considered.
I highly suggest planning everything out in as much detail as possible before you start purchasing anything. You'll save time, money and frustration in the long run.