Channel Tools is doing something but no audio is coming in on the plug in meter

If you recorded both microphones to a single stereo track, you don't need to route it to a bus for decoding. Just put the Channel Tools plugin right on the track, click the Mid-Side button under "Input Mode" and you're done. (Keep the track panned center.)

Whether you record to a stereo track or to two mono tracks routed to a bus, you should see a signal at the plugin's input. Possible reasons for having no signal...if the two microphones were wired in opposite polarity, you'd get a very low signal, so that's one possibility. Question: if you bypass the plugin, do you hear anything or see the meters move on the bus? If not, it could be your routing is incorrect. 

Check the track and make sure it's a) a stereo track, b) its track interleave is set to Stereo, and c) you didn't somehow combine the two mic channels when recording.