I'm sticking with the RJ45 jacks. I did some research before beginning the layout, thinking there must be something out there that is economical, flexible, and mostly smaller in size. I actually only need 4 signal lines, maybe one ground. What I found was that IDC is not small and has limited standard configurations, which were either too few or too many conductors - and still larger in size. The only option that looked possibly promising were molex-style connectors - but that would require a crimping tool and 128 robust crimps.

I also have been concerned about crosstalk between signals in the same cable. While not using the same principal of ethernet signaling (balanced line, common-mode rejection...) using Cat5 cable with signal/ground wire pairs and different twist rates seemed like it may help. So I'm going with the ubiquitous Cat5/RJ45 setup. Good point above about inviting incorrect connections - but in this specific case there aren't any actual ethernet lines running to the controller.

I've also modified the layout to include the RJ45 jack mounting tabs as part of the ground plane. I will also consider epoxying the jacks to the board to prevent ripping the traces off during disconnection of the plugs from the jacks.

Thanks for the comments.