are you in a hard-water area? Some people like to pour a can of coke around the pan last thing at night and before leaving the house in the morning, saying that the acidity breaks down the scale.
as well as a photo of the stains, please open the cistern lid and show us the inside. It will be useful to see if there are rust marks or scale, or peat stains. If the marks are green, from copper, it will be very difficult.
Presumably you have already tried an intensive toilet cleaner such as the Harpic "power plus" liquid in the black bottle. They also market tablets, in a black carton, thrown into the pan, but these only work below the waterline.
Please don't put any plastic dispenser cages in the pan, they cause plumbing blockages.