Graph Tech Trem Nut PT 1200

As my first bass turned 33 years old, it deserved some refurbishing. Last not least, the nut was about to turn into dust. Actually, when I unglued it, it broke into 3 pieces...
Anyway, I took all the measurements, filed the new nut according to the neck radius and the desired height and glued it in place. When I restringed the bass, I immediately realized that the D string was lying way below the other three. After a couple of plucks, the impression was confirmed and the D string is unplayable (it keeps banging against the first fret when playing the empty string).
That's a pity because it sounds very good, way better than before (OK, the old cracked nut is not a proper reference here...) adding a lot of sustain.
I haven't sent it back because I modified it (N.B. I didn't touch the slots!), but eventually it turned into a waste of money.