My sons have not experienced separation pain but from reading here & elsewhere, it sounds like that's what it might be. Warm baths w/o soap may help. I think I've read of people using epsom salts in this bath but I can't be sure. If you are nursing, you might dab some breastmilk on his foreskin. You'd need to be cautious w/ that though as if he has or has had yeast issues, that may make them flare. A doctor may suggest bacterial cream but I'd caution against that unless they know (via culture) that the problem is an infection. Our genitals are suppose to have lots of friendly bacteria on them (like the rest of our bodies) and anything antibacterial will mess w/ that.
I'm sorry I didn't reply sooner. Just saw this on Friday. I hope he's better now.