This bug report addresses the initial issue only…
As it may have gotten lost in this long thread, be advised that if you are using XCode 8, code signing is not exactly the same as in XCode7, see: Migrating Code Signing Configurations to Xcode 8
Please let me know if this link does not address and resolve the code signing issue you are currently experiencing. If it does not, please start a new post as this one is becoming long and hard to follow (Be sure to restate the issue, provide repro steps and associated logs.)
Thanks!