Just the toilet, no where else at all?

Just the toilet.

Just the toilet.

Then it is unlikely your well is the problem. If you can fill a tub or a sink with water and no dirt the well is good. Take the lid of the tank, is there a lot of debris on the bottom and maybe the sides

There is allot of debris in tank and on sides.

Clean it as well as you can with a brass brush or scub brush and vac out the water with a wet vac or repeated flushing until there is no debris. I'd let the tank refill and add 2 cups of CLR and let sit over night. Let us know if the debris returns anytime soon