It sounds like you need to do a pouch evac on him, and flush his pouch to get rid of the dead babies. I'm sorry, but I can't think of what you flush it with right now, but plain seawater would be better than nothing.
To do this you need a small syringe without the needle. Put some tank water in it, gently insert the tip into his pouch and very gently depress the plunger. Don't try to blow him up like a balloon and don't get any air in his pouch. Then very gently suck the water (and hopefully dead babies) out of his pouch. He won't like it a bit, and you may have to do it several times to get them all. It's OK to let him rest between times.
I would also place him in a QT tank for a short time, with triple sulpha, and all the live food he can eat. Hopefully someone will chime in here with the preferred medicine for pouch evacs. Let us know how it turns out.