I finally found the air conditioning ports for the rear air conditioning in my 2012 Ford E450, Goshen body shorty. They are over a heat shield and difficult to see.
Note this particular E450 has two independent air conditioning systems, one is the original compressor installed by Ford and matches the one you see when trying to order parts, one compressor was added, and the fan belt is longer than a standard E450 to accommodate the extra compressor. They are not the same compressor.
The refrigerant lines from the top compressor, the one for the rear, go over the engine, down over the driver's side of the engine, then under the bus just below the floor but over a heat shield for the exhaust pipe. The high and low ports to fill the R134a refrigerant are hidden above that heat shield and near the front edge of the condenser, both caps facing outwards. Neither port can be seen at all without looking from the side to see over the heat shield, and even then only a portion of the caps are visible.
The information sticker for the added air conditioning system that goes to the back is located under the hood on the right side. That sticker is filled in with a permanent marker, hand written, and not perfectly easy to read.