You can also count 5,7,4,9 or any other fretts you can do N.H. with, but since you're pinching them you'll sometimes have to count from the bridge, which will be very hard to count while playing. that's why you'll have to memorize those spots approximately taking the pickups position as your guide for instantly doing a P.H.
You should be able to do P.H. with any decent distortion pedal, but for sure a very high gain distortion like 'DOD DeathMetal' or 'BOSS MetalZone' will help.
Also make sure that you have a high output pickup to catch those harmonics clearly.
If you already tried this with high distortion and you didn't like the results, then it's the pickups or your technique.
Keep practicing.