To be honest I get the impression that if they were given some sort of "do-over" they would go back in time and just rebuild the C's rather than buy the MP36's.
The cost of rebuilding the F40PHs was FAR less than what replacing them with new units was, which was the main reason they went that route. Another reason is that I don't think they were all that happy with what the passenger locomotive market had to offer, either. They regret scrapping the F40Cs and learned from their mistakes.
Unfortunately the Progress rebuilds are crap. They run great now (after several modifications) when they are working properly, but they break down a lot. In time the mechanical forces will get them to a respectable level of reliability, it'll just take awhile. Currently all the geartrains on the prime movers are being redone (under warranty) at 47th because they weren't balanced properly by Progress. They were having a lot of problems with auxilary generators and main generator bearings because of the improper balance.
The MP36s' issues are well documented, but we've had them long enough now that they are actually the MOST reliable engines in the fleet. Metra has done numerous modifications, and the HEP conversion will eliminate the biggest problem these engines had.
The fleet is so small it's hard to keep everything maintained properly, but over time they really have corrected nearly all the problems with the computerized locomotives.