Manual stretching into external rotation, or lay back, should not be done.
The only time I have seen it done was as part of a post surgery rehab and done by a professional.
Is your should sore or is it pain? Those are two different things. Figure out where you are feeling it specifically.
How did you throw? Off a mound? Long toss? Did you warm up before throwing? Have you been throwing before this or were you just getting back into it?