I decided to replace the lame plastic nut on my $29 Fullerton ST-3 strat style guitar. Guitar Center sold me a pre-slotted graphite (All Parts) strat nut. I was able to remove the stock nut, although a small chunk of rosewood came off in front of the nut (ie, closer to the headstock). I superglued that back on; at least it wasn't past the fret. Anyhow, I had to do some mild sanding on the graphite nut, as the depth was too great to fit in the groove where the nut sits. (see photos below)






Now, I see that the nut does not sit competely flat in the channel, and the strings, particularly the bass strings, seem to more or less sit on top of the nut. If I bend the G or high E string in the first few frets, the string pops out of the slot. I don't have fancy luthier files or anything.
Two questions:
1. Should I remove this nut because of the way it is sitting (not flush)?
2. Is there a way I can create somewhat deeper string slots with sandpaper or something to that effect?

Thanks!