J.C.
Hey I had the same problem the house I live in is old the toilet had brown spots in it also,but it was also at the top water started. A girl at work told me about the new Lysol that came out that it worked for her. I went and got some and tryed it and that was three weeks ago and I am still stain free. It is called Lysol POWER Toilet Bowl Cleaner.......Im a big fan of clorox and it didnt even help..........I was really not expecting it to work. I had some kind of lime away the off brand of the CLR and it would tone the color down, but this stuff worked great..
Good Luck,
J.