It probably will. My friend put a convertible top motor from a '66 Mustang in his '88 convertable. Bolted right in. But think he had to wire in the correct electrical connector. I doubt Ford has changed it. It works good and it's cheap.
A 2001 Pump/motor will not interchange into your 1989. In 1994 Ford changed their pump/motors to alternating current. Your Mustang requires a direct current motor. A pump from 1965 through 1993 will directly interchange, without having to do nothing. These pump/mptors have 2 "hot wires", a red and yellow one and on the end they have a "male/female connector. These pumps also have a black ground wire. The 1994 and up pumps also have 2 "hot wires", but their connector is totally different from the 1993 on down pumps. These motors also do not have a ground wire. Hope that helps, as I have reconditioned and sold over 400 of these pre-1994 pump/motors on Ebay to fellow Mustang and Ford convertible owners...Poosker