Is it iron that causing the stain? I would try Iron Out.
I wrote a post that might help you - https://chascrazycreations.com/how-to-clean-your-toilet-from-top-to-bottom/ If this doesn't work then maybe this post will help - https://www.thespruce.com/hard-water-stains-in-the-toilet-2719033
This is a great post on removing stubborn toilet stains.
Pumice stones will NOT damage toilet bowels. I have cleaned houses for 20+ years! Used plenty of pumice on many a toilet. Not sure if it would help with yellowing? You could try...
Good luck! Hope you find a solution.