Joe
There were a few different looks of the R40 The original slant version was designed by Raymond Loewy The same Loewy that designed the looks of the GG1 A real good explanation of the R40 can be found here https://www.nycsubway.org/wiki/R-40_--_R-40M_(St._Louis_Car)
One of the big changes that Steve mentioned was the GOH which stands for general overhaul Big addition in GOH is that air conditioning was added which changed the design of the roof. This is the big difference in the MTH models The original was pre GOH and the roof had these vents on it that tended to warp and look like waves The later addition MTH is a post GOH and does away with the stupid vents on the roof