The line you require is: "core.mainmenu.website": "Website",
You can't hide a menu item easily though, not without hacking the code.
I dont have a src folder in the phonegap build version? I have noticed that the similar code is in 38.js is this something i can edit here?
I suppose the other way is maybe use the non phonegap version and upload in the normal way in phonegap, would this still work?
Yes. The src folder is in the Ionic folder structure. Although some html files are in templates folder in Phonegap structure, but most of them are packaged in the build folder. So, you can edit them in Ionic structure, and after running "ionic cordova prepare ios/android" you can copy the build folder from inside www folder to replace the build folder inside Phonegap structure.
This is what I am doing now.