How can I make an after workout pain lessen?

I really hate it after I work out intensely, some part of my body seems to hurt a lot. It's always either my chest, deltoids, quadriceps, and or calves. I know the cause of this pain, but how can I lessen it? It's harder to do a stretch, and I can feel my muscles popping out ,which feel like a million tiny rocks under my skin. I should also add that I'm a 13 year old male. And I don't have a lot of athleticism in my gene pool. My Vietnamese family doesn't have any athletes, so I'm the first.