I'm relatively illiterate when it comes to electrical circuits, but what you've done here seems pretty amazing. Because of my illiteracy, if I had this problem I would consider just taking the motors out of the trailing A unit and converting it to a dummy. For my use, at least, a single dual can-motored engine would suffice for my pulling needs. I think so, anyway, given that I have single dual-motored engines pulling loads like six aluminum passenger cars and decently long freight consists without problems. On the other hand, if I had this situation and really liked the A-A set, I'd probably send to GRJ for a complete makeover. 
Out of curiousity, I have a K-Line A-B-A set with the two A units powered, but the engines don't have cruise control. Just to confirm, it is just the presence of the K-Line cruise that creates the problems, and adding ERR CCMs to a pair of K-Line A-A engines without cruise would be a straight-forward installation of the CCMs, wouldn't it?
