What did they do with them when the MPI MP-whatevers arrived?
In a nutshell, F40C's 611 and 614 were retained, and continue to be stored serviceable by Metra, while the rest were sold to Helm, which then leased them to KCS. Meanwhile, a rather extensive discussion about the F40C's can be found scattered about on the older pages of this forum, but the links below should prove to be particularly relevant to your question...
http://railroad.net/forums/viewtopic.php?t=10347
http://railroad.net/forums/viewtopic.php?t=10983