Here is how I went about making this ship hold oxygen.
Hope this helps others design smaller ships.

1. The cargo containers/conveyors/connector/collector are the stock Business Shipment design, minus the Assembler.
   
2. The oxygen tanks were positioned in the corners, against the cargo containers. They are not in direct contact with the walls.
   
3. The Oxygen Generator was placed where the Assembler once was (on the roof). It's not airtight so two Walkway plates were placed on the inside against it.
   
4. A wall section was removed to gain access to the Conveyor Block behind to the Connector. The Vent then fitted nicely into that space.

So this is how you fit a working oxygen system and cargo storage into a 5x3x3 space.

The rest of the ship was simply a matter of fitting a double set of doors for an airlock, and building a space for the medical room and other facilities.