Motors are all the same.
The motor looks the same but is wired differently in the motor. Both have two leads to the main harness. The two speed has two internal windings, one for low speed, one for high speed. The two speed windings are also grounded at the motor. The three speed winding is not grounded at the motor.
I have a May built SJ FB and was looking to get some new harnesses. Im not sure if I have a 2 or 3 speed heater. Im unsure about which speed wiper I have, is there a easy way to test. I have attacked a picture of the wires going to the heater motor.
The switch is different as well. Two speed switch is: low; off; high. The three speed is: off; low; medium; high. The heater box for a three speed has a resistor mounted very visible from under the RH dash, the two speed has no resistor.
I strongly suggest you get a set of Mustang Assembly Manuals for your 65 car. You will also need a 64-65 Chassis and a 64-65 Weld and Sealant to be complete.
Jim
Jim