John you mentioned that you chnaged to shielded wires. All it takes is a single (missed) strand of the shield (connected to the core) to create a short.
If not already done, remove the connector(s) from the EC2 and check with an ohm meter between each pin on the connector and to ground (for pins that don't go to ground) for shorts (0 ohms).

Just an idea...

John,

I jus now realized that you used shield wires, did you shield all wires?  Don't know what type of wire you used, maybe you mentioned it somewhere.  Shielded wire can have a lot of capacitance and can make a signal all but disappear to an input. I don't know the frequency of the signals going to and from the EC2 and EM2 but maybe some one can fill us in.  You can see a low ohm resistance when measuring a cable but it doesn't necessarily mean the signal will get to the end at a usable level. Just groping for ideas.

Wendell