High Fidelity signal chains can expose flaws in technique and it happens to me ALL THE TIME when I upgrade anything from pickups to speakers and everything in between. It's not just that it's FRFR, it's that you're finally getting an accurate representation of the sound you're creating with your guitar. In a few months, your chord changes will clean up, provided you make an effort to do so. That string scratch sound is created by moving without lifting your fingers up all the way, so go back to fundamentals of fretting/releasing and try to do it slow without the noise. Anytime I'm having issues like that, I always try to return to fundamental technique exercises for a solution.
Also, I'm very fond of Elixir strings. A lot of people I've met that have tried them on their guitars don't seem to like them, but I went through about 10 brands and decided the Elixir's were my fav, not only for tone, but they last longer and don't rip up my fingers so much. On the other end of the spectrum for me are Ernie Ball's. Those things are like little tiny chainsaws.
