ERROR ITMS-4088 - Does not have permission to modify the application

SOLVED: Product->Archive->Export->Save for iOS App Store. Close Organizer and go to Xcode->Xcode(Menu)->Open Developer Tool->Application Loader, then sign in with your iTunes connect account and choose ipa.

This one worked for me:

https://devforums.apple.com/message/1056570#1056570

Using the ITC Credentials with the Application Loader

Go to Xcode. Preferences/Accounts.

Make sure you have logged in with your Company Account. The within your project go to General/Identity/Team and set your Company Team.

This worked for me.