I kinda know what you're talking about with the soreness. I have a tender scalp and something that I learned this month(4th month) is that although you may be tempted not to separate- do it anyway!!! You're just going to have a REAL mess on your hands if you let it go on for too long and then scissors have to be involved. And to keep those locks in check from getting in each other's business here's what I've found works:
Pretend you're putting your hair up in a pony tail. Grab a small cluster(four or five) of locks and move them up in the direction of a pony tail. If you feel odd pulling going on then you've got to narrow down which lock(s) are causing the discomfort. Once you narrow down who the naughties are then you can look at them individually and decide what to do. Most of the time you're going to have to pull a few hairs out(not OUT, just ... away from) from that lock and then loosely spin those loose hairs around a neighboring lock to get it out of the way. They'll eventually decide the best place to go.To decide which hairs need to be taken out of that lock, move the lock in several directions and see which way it 'pulls' badly and painfully. If it hurts to move it to the right then the offending hairs are much more than likely on the left. Same thing with north and south. Sometimes there are loops that are just pulling funny.
If you've got a few really naughty locks that chronically do this then I'd suggest putting a bead near the upper 1/4 of the lock to keep it from getting so hungry. Say you have four locks that eat eachother, put a bead on two of them. That'll let the other two mature a bit more and then in a week or two you can switch which locks the beads are put on. I have a cluster of locks on either side of my head which do this. Obnoxious as hell but at least I found a way to deal with the little buggers until they sort themselves out.