Both coal and oil are formed from organic matter (dead plant and animal material). The organic matter is buried under layers of sediment and put under intense heat and pressure. This prevents it from decomposing properly due to the lack of oxygen. After millions of years, carbon-rich deposits are formed, which we use as fossil fuels. To distinguish between the two, I think coal is formed only from plant matter (mainly trees) while oil may be a mixture of both animal and plant material.
Limestone is a sedimentary rock, which means it's formed from layers of sediment being consolidated under great pressure for millions of years. Sometimes, the shells of marine organisms become part of this sedimentation process. These shells are largely responsible for the presence of calcite (calcium carbonate) in limestone.
I'm not sure whether I've danced around your questions a bit there, but hopefully that's of some use. Can't answer the last one though, sorry.