Black staining inside toilet bowl (From a Rubber Part???)
Hello R Bell,
I would first check to see if your incoming flexible water line, the braided one from the wall to the toilet, is starting to break down inside. It's possible that your water has some trace minerals that are reacting with your home's copper water lines. I'm assuming you've got copper pipes, simply based on the color of the stains you're seeing.
Typically, the stains will be either a green/blue or black color when certain minerals are present in the water supply that is flowing through your copper pipes.
Further, I would suggest that you might want to look at the water connection coming from the wall or floor, to your Toto toilet, as you might see some staining inside the valve and hose. Just be sure to turn the water valve off first and have some rags handy to soak up any spills.
You might also want to have your water tested (most Sears stores do this for free - they use it as an opportunity to sell water treatment systems and softeners). Just get the test results and tell them you'll get back to them later. You might discover that you have some trace minerals that are reacting with the copper lines and that is the source of your stains.
To get rid of the stains, get some CLR at any home improvement, hardware, K-mart, Target, or such stores. This will disolve and remove the stains so the toilet looks like new, without harming the finish one bit.
I would also suggest that you might consider changing the water supply flexible hose from the house to the toilet, just to be covered, as it might be failing too.
Your toilet doesn't use a standard Flapper valve, so don't go tearing the integral valve apart looking for a black, rubber like material - there isn't one in the Toto Neorest line. It is a very nice toilet in both looks and function and you don't want to tear into a $5000+ toilet unless you know what you're doing. Save yourself the aggravation and time, as you won't find anything inside the toilet casing the problem.
With such an expensive toilet as you've got, it shouldn't be an issue of having it clean and functional without anything more than a normal, periodic cleaning. There are some inserts (neutralizing metals) that you can get to offset any water issues. You'll need to go to a better plumbing fixture supply house to get them thou, so save that for your last resort to resolve the problem, as you'll need the water test results to get the right ones anyway. Think of it like pool chemicals to keep the water balanced, etc. (that's an over simplification but you get the idea)
I hope you find this Very Helpful and best regards!