Con is it possible to Bypass the Rpi that is controling the BJ's and Sierra's and run the boards entirely controlled by a PC or Laptop, maybe it is the pi that is causing the unstable nature of the systems
sure , you can run it directly from a pc or a laptop, where cgminer is running , that's not a problem.
You can run it off any PC, and that's preferable anyway since the RPi is a piece of shit. Just plug in a USB cable. The sierras don't even have one so you have to run them via USB. Any instability still around is firmware related and remember it's still early days since release (even though release was late) but once my sierra is running it does not miss a beat.