I can say something about the "E" from memory. I think when the designs so designated (one radiator fan instead of two, cab that looks disturbingly similar to an EMD "Spartan" cab) were introduced (1987) GE said that the E was for "enhanced" in its press releases.
As for C-41 and C-42... GE has been quite sloppy in what it puts on builder's plates, so I don't know if these units came from the factory labelled as C40 or with the higher numbers. Certainly they were referred to as C41 (etc) at the time (1993, maybe 1992), but I'm not sure whether that designation came from GE, from the railroads, or just from the press.
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While we're at it: is a C42-8 the same thing, or at least the same power rating, as a C41-8? As I recall, it was announced that an order of C40-8 for C&NW was being built at a 4200hp rating (I think it was actually a bit less and the designation was "rounded upward"), and that this order was the only one of units called C42-8. UP and ATSF got C41-8W in 1993; I think they are rated at 4135 hp. Are they really different from the C&NW units?
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And, just to complicate things, CSX 9000-9002 (the first three of the units that are variously called C44-8W and C44-9W) were announced, before they were built, as being 4500 hp. Were they originally built to a bit higher hp than that subsequently settled as standard for Dash-9, or had 4500 turned into 4400 (or 4390) by the time they left Erie?