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I am sorry to hear that Warren if not feeling well. Unfortunately, non-specific pain can be difficult to diagnose, especially in a puppy with no history of other signs to help localize it.
My list of possible differentials in your dog's case includes such things as meningitis, immune mediated polyarthritis or a growth disorder of the bones (panosteitis, hypertrophic osteodystrophy, etc). Unfortunately, these things can de difficult to diagnose unless one has a high index of suspicion for them. I see them quite frequently so they are at the front of my mind when i deal with a painful puppy. I recommend having him evaluated by a specialist if your vet is unwilling or unable to consider these differential diagnoses. Testing recommended includes joint taps to evaluate joint fluid, x-rays to evaluate the bones and growth plates, blood work to look for evidence of inflammation and possibly CSF tap (spinal tap) and analysis to start. These tests may or may not be performed by general practitioners as they typically require some skill in performing them and interpreting the results. If there is no specialty hospital in your area or you are unable to have the testing performed due to financial or other reasons, you can discuss a trial of steroids with your veterinarian. Steroids such as prednisone may be used as first line therapy for diseases that involve immune mediated attack (meningitis, immune mediated polyarthritis and some of the growth disorders) or sufficiently suppress inflammation to help reduce pain. There are down sides, however and if there is an infectious cause that is the source of the pain and discomfort, using steroids may make him worse. Further, if you decide to pursue testing after starting prednisone, then you may not get clear results. There are pros and cons and I recommend discussing this with your vet before making a decision so that you can make an informed choice and explore all of your options. For pain on an outpatient basis I like to use medications called gabapentin and tramadol. Because a non-steroidal anti-inflammatory cannot be used with a steroid, you should also discuss using one of these medications with your vet in lieu of steroids. These are very effective pain relievers.
I know this is a lot of information and I am happy to answer additional questions you have if there are any. Have I been able to address your concerns satisfactorily tonight?