You have a masters in CS and 6 years of management experience. You are so far from fucked.
Also I wouldn't give the Founders the benefit of the doubt of being "good people." Even if they are a YC startup, morons come in all shapes and sizes so even YC isn't moron-free. And yes, only a moron makes decisions to hire people that will have to go through a lot of change to take the job without being absolutely positively sure that they are the right person.
This sounds like an episode of "Hire Slow, Fire Fast", which is a cool way of saying: "We fucked up. Abort! Abort! Abort!" Despite how nice they are being to your face, they've realized for some valid-to-them reason that they made a mistake in hiring you. Don't take it personally, just get back on the horse.
Really. Employers everywhere are looking for people like you. Breathe, accept what happened, DO NOT BLAME YOURSELF FOR IT and move on to the next thing. Remember, if you are going through hell, keep going!