Strange... Current version of Xcode live in /Applications, not /Developer. The only thing in my /Developer is related to NVIDIA CUDA-5.0. Copies of the PluginManager framework also live in FCPX, Motion, Compressor, and iMovie. Don't know if they are the same version, though. Probably not.
Glad you got it working. FWIW I updated to Xcode 5.0.2 and had no Aperture issues.
Not sure if you have solved your problem yet but after a couple days of pulling may hair out I found a simple solution that woke for me. Simply reinstall the canon E1 plug in for mountain lion and it all works again.