Need help with a toilet repair!?

We have a Kohler 1.6 gallon toilet. Forgive my terminology, but the toilet runs every 5 minutes or so and I think it is due to a leak somewhere around the flap at the base of the tank. I unscrewed the tank from the toilet itself and replaced the the flap and the "pipe" that connects the tank to the place where the water flows into the toilet. When I reconnected it, not only was it still leaking into the toilet, but now there is a leak where the screws went in. There is a triangular piece of rubber that plugs the screw holes and fits around the pipe that goes into the toilet. Do you think that is the problem and where the leak is coming from? If water is coming through the holes where the screws go, does that mean I need to buy something else to help plug the hole? HELP!! Thanks