There's a good chance that there's a fact lurking there we don't see.
Did you propagate the blue dye all the way through the water in the tank, or did it just collect at the bottom? I had one of these a few weeks ago where the poster said he used dye and none of it ended up in the bowl. When we found a crack about an inch from the top of the overflow riser, he allowed as how he hadn't mixed the dye uniformly through the water, because he was focusing on the bottom of the tank. So...was all the water in the tank blue, or just some? Did you leave it all overnight and the water still went down but none ended up in the bowl and none on the floor?
As you have adjusted the water downwards, has it fallen 2" each time, regardless of where it starts from? If you left it longer, would it fall more than 2"?
Does it fall to the same place each time? Or is it a firm 2" regardless of where starts from?
This may help us find a solution. I would use food coloring well-mixed in the water to test.
I know that Mansfield has an adapter for its flush valve to help prevent siphoning, but it wouldn't be necessary with a flapper-style valve. When you had the flapper-style valve in, did you have the refill tube daylighted over the top of the overflow riser?