|Keep It Simple, Stupid|
I can see where some of these may actually contradict each other. For example, "Do The Simplest Thing That Could Possibly Work" often means "cut and paste" which is the exact opposite of "Don't Repeat Yourself"
Rather than looking at them as contradictory - look at them as working together. Doing the simplest thing that can possibly work might be to copy and past something. Which gives us a code smell of duplication since we should do things once and only once. However since we refactor mercilessly we'll quickly remove that duplication into some kind of common abstraction. So we have clean code. Problem solved.
These are not things you do in isolation - you do them all together all of the time. Doing the simplest thing that can possibly work is a starting point not an end. Synergy is a wonderful thing :-)
Refactoring is not the simplest way to get things to work
I used to think that. I don't anymore. I've found incrementally growing and refactoring a framework to be an enormously effective way of developing flexible high quality applications.
Further, I really have to disagree with your first one: "You Arent Gonna Need It" … You don't get this type of flexibility by writing code when you need it, you get this type of flexibility by writing a framework that does it already.
Colour me slightly suspicious with your diagnosis of the fault with your first system :-) Why was the original project so hard to change? Was there duplication? Was there scope for refactoring? How did you know what flexibility you needed to add to the second system? Were there requirements that weren't made explicit in the first system? Etc.
The reason I'm suspicious is that the flexible framework that you describe is what I'd expect to produce by following YAGNI and the other practices I briefly outlined.