The blue wire heads to the #3 position of the bulkhead connector which is the 10 o'clock position (from the engine side) of the the bottom 4-wire connector (under the wiper plug). The green blower wire in the engine compartment comes from #4 which is in the 7 o'clock position on that same plug. As you noted on an earlier post, the light green wire (C1C-16LGN on the diagram) is coming from a tan ACC plug under the dash.
I don't see how these wires could get switched.
Just wondering: if you disconnect the three-wire resistor plug under the glove box, does the fan still run?