I ***think*** (my memory was always fallible and isn't getting any better with age, and C-39-8E production was twenty-nine years ago!) that the change from C-39-8E to C-40-8 involved a new turbocharger, not just a change in the control software. But check with someone else before betting money on that!
There is one visual difference: the C39-8E had the air reservoirs in the conventional location (mount crosswise on the frame, one before and one after the fuel tank), whereas the C-40 made the change to having them mounted in an indentation on the side of the fuel tank on the right side.
Neither is a really MAJOR major difference. Given the overall similarities, however, perhaps the C-40 amounted to a refined and thoroughly debugged version of the C39-8E: maybe the C39-8E got blamed for what were in effect teething troubles for the design? (But that is sheer speculation on my part with nothing to back it up.)