My go to for stains is a pumice stone! If you are lucky, you can find one on a stick but they are not always available! It works amazing though to bring your toilet back to looking like new!
I had a problem with hard water and after emptying the bowl I added about a quart of vinegar and let it sit for 5 hours. Then used a toilet brush and flushed away the mineral deposits.
Professional grade CLR (Calcium, Lime Rust removal) work wonders.
Try sprinkling baking soda and vinegar in bowl and use toiletbowl brush and let sit awhile then flush