The whole pickup height thing for me was a bit of a learning curve. One thing I learnt this week though since installing a new set of Mules last week, is to give your guitar a good going over through the set up you play live.
At home I have a cr@p practice amp, and it was with that I was initally setting the height of the pickups. Thought I had it nailed, until I went into a rehearsal room on the weekend on my own.
I plugged into my live rig, and was surprised by how it sounded - strings choking high up the neck, muddiness etc.
So I began a slow process of lowering the pickups, half a turn at a time - playing some chords, small lead runs, then making another half turn and so on - took a little while, but the results were fantastic.
I dont really have the opportunity to play through my live rig at home due to wife/kid/neighbours. But it made so much difference to me to actually set the pickup heights using the exact set up I will play live.
Just have to say, the Mules sound great - especially the bridge pickup. So much fun to play - and playing on my own in a rehearsal room, with the amp CRANKED was so much fun, highly recommended to other guys out there who are restricted to volume levels at home.