So you were correct, most likely a transmission issue.
There was a Ford TSB for 2000/2001 Rangers about the connector under the drivers seat.
This connector passes several system wires from inside the cab to outside the cab.
There was a problem with this connector getting water inside.
On this list
All TSB's For 2001 Ford Ranger
This could cause transmission issues, speedo issues, ABS issues, ect.....