The best way that I have found to get stains out, is just thorough daily grooming, but I don't have running water at my barn, so I've had to just groom through it. I'm sure that someone on here will have brilliant ideas of how to get the yellowing out of her coat.
As for the rubbing when she is in season, she must be itchy. I've seen a scratching mat that can be hung on a stall wall or wrapped around a post in the pasture. It is supposed to give the horses a safe place to rub, with out the cuts, scraped, and pulled hair. I was it in one of my catalogs, but can't for the life of me find that catalog right now. You could also try washing her rear end to remove the discharge caused by her heat cycle. If she's not itchy, she shouldn't rub her tail out. As for re-growing it, just keep it well conditioned and protected, either by braiding or whatever method you prefer.
Good luck with her tail and the stains.