I found a page on a really small "refinery in a box" for third-world nations:
http://www.almonerpetrogas.com/Mini_Refineries
It looks like a lot of it fits in one prefab "butler building", plus a cooling system that looks a lot like a large shallow pool of water. They state only 1 or 2 workers are needed to operate it. They give capacity as 900 tons per month per skid; a metric ton of crude oil is about 7 barrels, so that's about 200 barrels production per day. The plant capacity is given as 200 barrels a day on up. The equipment is shipped in standard 40' ocean cargo containers; if one skid = one ocean cargo container, then the smallest plant is all in one container.
So: for just one container you get 40% of the refining capacity of a 9 container plant; but I suspect this one-container refinery is less safe, produces products not up to the same specifications, won't last as long, and more environmentally harmful. But: much smaller.
If the Project "stocked" these, they'd probably have 4 or 5 containers: one for the refinery itself, and 4 with all the other parts that the "end user" would be expected to provide pre-Atomic War, and the tools for assembly.
Site selection might just be "find a surviving big building near a river or lake and a supply of crude oil."
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Michael B.