I am having the same issues. I have 4 Makerbot Replicator 2's.
Please let me know if you work it out. Im using OS X 10.11.2
Meanwhile, I've found some informations and customized the Printer file.
First you have to stop the backround service "Makerbot Conveyor Service" installed by the Makerbot software on PC
or "Conveyor-svc" on Macintosh.
May be the best option is to open MakerBot software on Mac and ask in "service" menu to stop background services...
Next I have had to modify the "USB signature" in the "makerbot replicator 2.3PP" file in the "3D printers" folder.
in order to make my PC recognize something.
|<USBID VID='23C1' PID='B015'/>|
<USBID VID='23C1' PID='B016'/>
and also, even if the rep 2 own only 1 head
<PrinterHeads value='2' />
after that I get some answer from the device.
Let me know if it works for you