I had similar logs as the OP, with Connect: Couldn't Start AFC service, and System.IO.IOException: AFCFileRefOpen (/PublicStaging/MyProject.ipa) failed with error 7. This is UE 4.9.2, OS X 10.10.5, iOS 9.0.2, iPad 3rd gen.
I fixed it by disabling wifi on the iPad, unplugging the cable and plugging it back in, and re-deploying. I presume that the first time it was trying to sync over wifi even though the cable was in. I don’t know if I’ve ever had wifi sync work (I’m new to this) but cable sync seems to work fine.