Plumbing – What would cause a toilet tank to intermittently leak into the bowl only when half-full or more, even after a flush valve replacement

From what you have said, it sounds like a better way to go might be to replace that top edge of the brass outlet pipe. They sell kits in the store to replace the flapper valve and the seat (which is what you are struggling with). Have you looked into one of those? Something like this:

http://www.amazon.com/Lavelle-2003BP-Flush-Valve-Repair/dp/B001ARJR8S

Trying to sand the existing seat down, in place, until you get a good seal sounds like a lot of work with little chance of success. With a kit like this, you seal a new plastic seat down on top of the old one with a silicone sealant, then the flapper seals against the new seat. If one of those seat replacement kits will adapt to your toilet, that is your best bet, in my opinion. Hope this helps.

The overflow tube drains directly into the bowl, not the tank. The only way I can think that it would prevent the tank from filling is if it was cracked or had a hole in it and allowed tank water to drain into the bowl. If this was the case, you would notice the fill valve cycling if it was a slow leak or never shutting off if it were a large leak. The reason the tank fills quickly when you divert the bowl refill tube into the tank is that you are simply not splitting the water from the fill value between the tank and bowl any more.

It sounds like your fill valve assembly is the problem. The fill value has 2 outlets, one that directs into the tank, and the other that sends water into your bowl refill tube. My best guess is that something inside of the fill value got clogged with sediment, hard water deposits, or something else that restricted it. These are relatively cheap to replace and likely not worth the time to clean them out in my opinion.