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On one of my last builds I placed the bridge position pickup too far away from the bridge. the only way I get good tone out of it is if the guitar is tuned way down, and I skew the amp settings way way out from what I usually use on my amps. even then, it is too bassy and muddy. not very powerful sounding. the pickup in question is a Bill Lawrence USA L-500XL. in a mahogany bodied, neck-thru super strat. I haven't played with pickup height much, and I'm not sure if this would improve on the tone, or make it even bassier if I brought it up closer to the strings.
In retrospect, these pickups may not have been the best choice for this guitar, but I had them around, and this build was for personal use and budget was very limited. I routed the cavities to mount them directly to the body, and to fit tightly around these pups. I wish I had placed this closer to the bridge, but it's too late for should'ves... Is this something I will just need to deal with, or will adjusting the pickup height closer to the strings improve clarity of the pickups? they are currently both at the lowest settings. if not, I will route a new cavity closer, and try to design some kind of pickguard to cover the old cavity.

Play with the pup height, that's an easy way to change the balance and/or increase or decrease output (volume not voltage readings).

You still may have issues with liking the tone of the guitar and/or pups but until you play with the height you won't know for sure.

Also be careful not to get too close to the strings with the pups which can cause other issues if the pups have powerful enough magnets. Not sure if Lawrence lists a spec for how close you can get to the strings but that would be something that I would want to know and heed.

It could be that a quick height adjustment could get you where you wish to go. Let us know if this helps?

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Ann Arbor Guitars

Longtime Lawrence user here, and don't get your complaint at all.
They have a proven track record of fidelity, clarity, and power.
Maybe you should define "good tone".

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"Act your age, not your shoe size" - Prince

Well, by good tone, I mean this thing just doesn't sound pleasant. The bridge pup sounds too loose, and way too much bass. Not real tight sounding at all, and doesn't cut through. I messed around yesterday, changed the strings and the bridge, and added height adjustment springs, but haven't yet had a chance to plug it in to see if it's improved

The tonal descriptions used are extremely subjective, and very difficult for readers to reliably translate in their minds as accurate to what you are hearing (especially in terms of degree). What I gather though, is simply that you wish it to be brighter, greater treble response than it currently has.

Before routing it out and moving it, how far is this pickup from the bridge? What other guitars/pickups are you comparing to which you wish to better emulate? Is it wired through a standard volume/tone arrangement with higher value (500k or more) pots?

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Eschew obfuscation, espouse elucidation.

I use the same pickup in several other guitars. This one is approximately one inch further away from the bridge than normal. It is wired through CTS 500K pots, with a typical ceramic capacitor on the tone pot, .470uf. Switchcraft Jack and switch for any difference that may make.

Yes, I do wish for greater treble and midrange response. The other guitars I have this in sound so much better. They sound like two very different pickups when I switch guitars. And the wiring is correct.

Gotcha. Yeah, unfortunately I think your initial assessment was probably correct, and it's likely you're going to have to route the cavity and move the pickup back in a pick guard mount. A full inch further from the bridge is certainly going to shift your tone away from the typical bridge position sound.

And I assume you meant .047uf for the cap rather than .470uf, though until you turn the tone down this wouldn't make a difference anyway.

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Eschew obfuscation, espouse elucidation.