Gunnar did a similar thing, and I was able to isolate it to a single pad on his foot. It took a lot of pressure from my hand to elicit the cry of pain from him that told me where the pain was coming from.
My suggestion to you is to look at a diagram of the anatomy of your dog and deliver firm pressure to every joint and growth plate in his sore leg from the shoulder blade all the way down to the toe nails. If you can find the source that gives you some insight.
Also, a new vet might be in order. Pain killers cover and issue, they don't solve it. I'd avoid those in a puppy.