I would see a neurosurgeon and get a thorough spine evaluation and an MRI of your whole spine. Blood tests such as ESR, uric acid and rheumatoid factor should also be done. Your pain could be from degenerative disc disease (DDD). Simple physiotherapy and taking glucosamine could be helpful while you getting these evaluations done.
You should go to see doc for neck examination.
I don't think kidney stone and liver problem can lead to your symptoms (neck ,back,knee,shoulder).
Good luck!