I've been wrestling with the same problem after upgrading from Xcode 5 to 6.0.1. Trying to load my large and complicated iPad storyboard would freeze Xcode, bring up the Pinwheel Of Death, and eventually crash it out. Sometimes it would show errors on build as well, mentioning missing OIDs.
I ended up rolling back the Storyboard file in Git (via the command line since Xcode wouldn't let me get that far) all the way back to the very first straight-from-the-template version. I cleaned the project and rebuilt it, and the storyboard loaded properly.
I then went forward in time commit by commit, cleaning and building every time. I expected I would get to a point where things broke again - but I got all the way up to the most recent commit without any freezes.
When I tried jumping ahead by several weeks, though, I got the freeze-ups and crashes again.
I wonder if the new Storyboard editor in 6.0.1 just needs to build up its internal representations (and caches?) in smaller easy steps rather than the giant leap of a full complicated file.
This rollback/roll forward/rebuild process took about 45 minutes for me, but that's a whole lot less time than it would take for me to rebuild this storyboard. Hope this helps you.