The plumbing rough in is where they put the main plumbing lines coming in and out of the house. The stem wall was dug under for passage of the PVC pipes. There is a trench that houses a large water line that all the extra water and waste drains into from the rest of the house.
The stem wall is a concrete outer wall that forms the boundary of the outside foundation. This will be filled with plumbing and finally concrete. All this will form the foundation. The wood frame and subsequent house will sit on top of the foundation.