On Mon, 21 Dec 2015 13:18:55 -0600, Muggles wrote:

My first and only idea is the area where your trying to get the seal is
slightly pitted somewhere, and won't seal because of where it's pitted.
Maybe it can be sanded down where the seal is supposed to be at? Is
that possible to do? Like someone would put a bondo on a car and sand
it down to smooth it out, put some material around the hole, let it dry,
sand it down and then it might make a seal?

The OP has already replaced parts that would be "pitted". Something
else is going on. He hasn't addressed a "possible" hairline crack in
the tank or bowl, at the gasket.