After having a week long discussion with Phonegap and Apple the issue has finally been figured out.
Found here:
http://community.phonegap.com/nitobi/topics/error-itms-90034-missing-or-invalid-signature
So I finally found out the issue.. The issue wasn't with the certificates, after i built the project in cordova for ios I opened the xcode project. Trying to submit the app through xcode also didnt work. So through xcode I validated the project and compiled the api file through xcode instead of phonegap and from there used application loader to import to the appstore. This solved the issue. Maybe this is something phonegap need to look into since i shouldnt have to use xcode to compile my api file..
Also another thing i found was that itunes connect would be funny with app ids i created if i was using chrome. Had no issue when it came to safari.
So summarising, use safari when dealing with apple services (Annoying becasuse you do expect to use them anywhere) and I built the project in ios (cordova build ios - command), opened the xcode project it generates, then create the ipa file through xcode:
Step by step shown here: How to use the C socket API in C++ on z/OS...
Before making the ipa file make sure you validate your app through xcode - this is very important.
Then using the ipa file it generates, use that in the application loader.
Im glad the issue has been solved but phonegap build needs to be looked at, i know it wasnt any other issue as xcode compiling the api file is the only difference in the process that works.
Thanks for the help