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Using pickup shells bigger than pickups

@Geoff_tcf
Not sure what P2 size is but I needed to swap pickups and rosewood covers were the answer. It was OK with the humbucker as it was a snug fit,for the single coil I centred it within the box then placed foam in the gaps. Course it hepled they were blade types.

I wouldn't worry about being dead centre over the magnets,it's mostly an OCD issue. Plenty well respected basses out there strings/magnets don't align.
 
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@Geoff_tcf
I think Haroldo means like some humbuckers are mounted on guitars. The height adjust screws go into a cradle hidden below the scratchplate. Course if that's the case you'd just cut a bigger hole.

Oh here's a couple of photos from me using the wooden boxes.
Zephyr pickups (1).jpg Zephyr pickups (2).jpg
 
Out here in the world of custom bass building, we commonly fit custom coils into standard covers. Usually we use strips of wood to fill up the gaps at the sides and ends, and hold the coil centered. Then pour in the epoxy to fill it up. That's the solid, permanent way to encapsulate a pickup.

If you want to do a temporary test installation, use the wood strips and double-sided tape.

Aligning the pole pieces to the strings is done by measuring. If the cover has already been mounted to the body, then you need to fit it in place and mark where the strings are. Fit the wood strips so they hold the coil in the right alignment. Yes, the pole pieces should be centered on the strings. You don't have to obsess to thousandths of an inch, but they should be centered.
 
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Look at MM5 pickups, eared or older SR5 style.
You'll notice the coils aren't that different, it's more a plastic cover redesign.

When I was wrenching 20 years ago there we would do coverups, like covering an old tattoo.
It's easier now bc there's a lot more options, instead of grafting on bits of one bass or another into a single instrument.

Glue guns are your friend.
I used wood or plastic shims to center the pickup under it's cover.