Re: A Perfect Circle/Opeth
I love those bands - good choice!
IMO look at the JB, Custom and Distortion. You need something with good definition/clarity (for complex chords) yet toneful, and a decent enough clean sound. If it was me, of the three i would go for the JB, but listen to sound clips and what others here say. The JB probably has the best clean tone of the three and still has a great distortion sound (i think the guy in Tool uses one, if im not wrong), the custom maybe has more definition. I have no idea what pickups APF and Opeth actually use.
If you ever change the neck pickup, I would get a lower output one like a 59. That would allow you to have a more versatile sound, better clean tones and warmer lead tones like those bands sometimes use.