Honestly, I've had the same issue, high pain tolerance, and I don't have a definitive answer. Half of the time, I stretch and wind up in pain the next day even if it didn't hurt when stretching. However, I have found a few things which have helped.
- Always warm up before stretching - It doesn't have to be much. Walking around the gym a few times while swinging my arms does it.
- Go slowly and gently into the stretch - It's very tempting, particularly when you "know" how far you can go into the stretch, to just drop into it. That's a good way to hurt yourself without even realizing it.
- Consider going by strain rather than pain - If you don't tend to feel pain when stretching, consider going by the tightness of the muscles and connective tissue. When they feel tight, pause in your stretch and only advance slowly, paying attention to whether things are feeling tighter. If your muscles start trembling, back off a bit, because, from my experience, that means they're hitting the point of failure.
- Learn your limits and only push a little past them each time - This one's a hard one since it's basically encouraging you to not strive to do your best, but when you find a depth of stretch that doesn't result in strained muscles the next day, don't push yourself much further than that on the next day. It's slower, but it will cut down on the damage.
- Be wary of holding yourself in a prolonged stretch - This is one I'm guilty of. The current wisdom is PNF stretching, going to a lesser level of stretching and then flexing there. Personally, I find myself combining that with a deep stretch, getting myself low and then pushing myself to hold on for "just a few more seconds". The adrenaline from forcing myself to hold the position often leaves me unaware that I really am past my limits.
I hope some of these tips help you. Let me know if there's anything else I can do.