You would be astonished at the amount of time that can be flushed down the toilet during your PhD. However, you have to remember something important: that's what research is. People get some strange idea that we always know ahead of time how an experiment will turn out. Nonsense, of course. If we knew what would happen ahead of time, it wouldn't be an experiment, would it? And every time one of those million dollar instruments goes down and you find yourself on your knees, elbows-deep in the cockles of random, unlabeled wiring, sometimes for months at a time.
Your PhD is not for you to show off how amazing you are to the community. Some folks have everything go right. Others don't. That doesn't make the person who had everything go right have a more valid PhD than the other. Ultimately, your PhD is about making the statement that you are a master in a particular field, and acknowledged as such by your peers. That doesn't always mean success. Sometimes it means tackling a problem in such a way as to make it easier for the next person ahead of you.
We all want to be the person who invents an FTL drive, cures cancer, whatever. Few of us will be. Few will become rich, famous, or particularly successful as a result of our research. That's how it is, and eventually (usually after the PhD) you learn to accept that.
It's hard to say what's best, to write more papers with less content, or fewer that were more powerful. The second would seem obvious, but it isn't. I knew a woman who got her PhD with something like 23 papers during that time. Which sounds amazing, and you would think she would be fast tracked for greatness. And you would be correct, her career continues in the Ivys, last I heard. But other folks sneered, since her papers consisted of "I changed the pH to 6 and wrote a paper" and "I changed the pH to 7 and wrote a paper" and you get the drift. But despite such sneering, she succeeds. So which is better? Clearly, hers was an example of a degree in which lots of things went "right." So what?
Your validity as a scientist has never been and will never be about your results. A PhD doesn't mean you are smarter than anybody. It means you had the luxury to dedicate the time to a degree. What a PhD is supposed to mean is that you have shown yourself trained in a particular manner of thinking. That you don't just plug the numbers in and read off the result. As a PhD, your job is to be he person who squints at the numbers, mutters under your breath, and tears the work even when it is your own and it tells you exactly what you want to hear to shreds.
So, for what it is worth, rejoice! Your post convinces me of nothing but that you are in a good place. Of course, it isn't easy to do-confronting an advisor with a screw up, facing this stuff, it's terrifying, humiliating, painful. But that's what it is to be a PhD, to have that ability to do all of this and walk through that fire, having the integrity to see what is true and what isn't, having the courage to pick your course, and having the strength to go through all of the slings and arrows that come at you when you go along that path.