I changed my mind on using optical for the filament detector since clear filament might be an issue. I think this idea below would be awesome if the bowden tube press in fittings could be threaded into each side.http://www.thingiverse.com/thing:1698397/#comments
Octoprint has a runout sensor plugin that runs to the Gpio of the raspberry pi.
I am thinking similar things about the extruder location. i am half tempted to just stand up a 3rd pillar to bolt it to.