I'm surprised you're having trouble telling one note from another - my RY is one of the tightest, most defined-sounding pickups I've ever used.
They're probably higher-output than your stock pickups, so they're overdriving the amp much more easily, at lower settings.
You probably just need time to get used to them, I know it sounds obvious but try turning down the gain on your amp (and/or distortion pedal). You don't necessarily get the best distorted sounds at the highest settings.
Can it be because they are to high?
Yes, it might be that the pickups are too close to the strings. If you lower them a little you'll get less output but the tone will be clearer.