Will CLR remove rust stains in the toilet bowl.

Yes, I've done it

Yes, this product will remove rust stains in the toilet. It will take time depending on the degree of stain.

Yes. Depending on how bad the rust stain is, here is what I do. Turn the water to the toilet off and flush the toilet. Once bowl has emptied most of the water, lay a layer (double layer if toilet paper is thin) of toilet paper over rust stained area and then gently, so as not to move toilet paper, dribble CLR onto the toilet paper. Wait a bit, check progress. If necessary, dribble some fresh CLR onto same toilet paper. When done, turn on water, flush.