all of this from someone who has ‘lapsed’ on the guitar, but there you go.
unless you have a medical condition you should find that endurance training makes any muscle group less painful, so it seems to me that although you are practicing, you are not practicing in the same way that you want to perform.
lowering the action might help, as would focusing on being ‘light’ on the strings with left hand no matter how fast or heavy you want to be with your pick hand. you often find that you can be really light when playing slow and quiet, but end up trying to squeeze the neck when playing fast or loud.
you cold also try lighter string. Is the back of the neck varnished? if it is then you might want to try a guitar with a sanded neck instead, less friction for moving the fret hand.