Yesterday (3/10/14) when iOS 7.1 was released I also upgraded to Xcode 5.1 and found that my PhoneGap/Cordova project would no longer compile to my iPhone 5s. I also upgrade
Follow the instructions on this video: https://www.youtube.com/watch?v=EIkJAKcz8DE
Just add arm64 in your projects valid architectures and remove all the conditional architecture of Cordova's project.