If you have the builder grade TOTO with 2" universal flapper, then it may be that whoever replaced the original flapper used a replacement and didn't cut the part off that goes on the overflow tube.
When replacing the flapper, make sure it swings freely on the posts.
You may have to trim off some of it with a scissors.
Any generic fill valve should work, either the Fluidmaster or the Korky.
Looking inside the Toto ST703 tank for the builder grade model.