mustang window and mirror backwards

I seem to remember that the 94-95 and 96-98 mirrors were physically identical, but the wiring in the plug was swapped. However, the swap meant that up & down was now left & right, and vice versa. Never heard about your situation. Do you still have your old mirror? You can compare the wire colors between the two mirrors and see if one is wired wrong.

If the wires are just in the wrong order in the plug, you can pry out the center plastic piece and carefully pop the individual connectors out - then order them correctly.