Sound like you might require further assessment of the hip at this point. If the x-ray was essentially negative and the current approach hasn't helped then it's past time to change approaches.

Go back to the GP and ask for an Wikipedia reference-linkMRI. You need to go to the physio when you are in pain or when you can reproduce the pain to help the assessment. It might be related to something in the back.

That said there are a number of issues about the hip and some are difficult to diagnose but 12 weeks with no results is 12 weeks with the wrong treatment plan.

As for the shoulder it is likely that if you are lame in the hip you will run in a way where you hold to mugh tension in the upper body (shoulders). Hip pain won't directly refer to the shoulder however running with a dysfunctional hip can lead to shoulder pain due to the bodies compensatory strategies.