Eric,
The easiest way to upgrade to MT couplers is to replace the trucks with either the Bettendorf(489-302026) or Roller Bearing trucks(489-302046 or 489-489-302047). The numbers I referenced come with low profile wheels. If you have to use another MT truck that comes with the deep flanges, you can use Atlas low profile wheelsets (150-22136).
Hope this helps!