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Pick up Height

I need just a little help over here.
I installed the fender custom shop 60s on my MIM fretless and i think i have much less output and low end compared to the stocked ones. Even though the tone was crispier and more accurate, I felt i was missing the low end i had before. I had to play on a studio amp and not mine but with my previous pickups volume settings with this amp were gain 5 vol 7 and now even with gain 5 volume 9-10 and beefed the bass eq i did not have the low end i had before and I was lost in the mix. Could this had to do with lower height of the pickups? I mean does pickup height could play such a big role in output and fatness of tone? I find it very hard to believe that my stock (at least neck pickup) has better low end than these custom shop ones.
 
The pickups have screws so you can adjust their height to get the best sound. Learning what these screws do is an essential part of learning to "set up" your instrument. :)

Official setup guide for Fender instruments: Invalid Link Removed

Also, it is totally normal for different pickups to sound different. If you swapped pickups without auditioning them first, then there is probably about a 50/50 chance whether you will like the new ones better or worse than your old pickups. ;)
 
Of course pickup height can totally change the volume and fatness factor. Research what the output spec is on your new pickups. They might be less than the stock ones. Sometimes it's worth having less output if the pickup reproduces more detail. A pickup can be louder but the quality could be worse. There's nothing wrong with letting your amp do the work instead of just the pickup.