ibtool fails to compile storyboard in Xcode 7.1 Beta
So thanks to an Apple support staff member, the solution is to move the Main.storyboard file from the Compile Sources build phase to the Copy Bundle Resources phase.
Adding another potential answer for "Error creating notification handler for simulator graphics quality override". I got this error when I added a run script in xcode build phases, and then dragged the script to the sop to make it run pre-build. No idea why this happened, but when I dragged the run script window back down to the bottom it fixed it.