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How you deal with a too loud B string?

The bass itself doesnt clip, it clips in comparison with the other 4 strings when they have a normal signal input
Yes, I absolutely understand, but the temporary and imperfect solution to the B string causing clipping that will not cause greater imbalance is going to be lowering the whole entire pickup. It will still be unbalanced, but at least the B won't be clipping.
 
I gotta say that in my experience this problem almost never occurs, and on the one bass that I have that does this ('02 Lakland 55-94) it's like having a wonderful secret weapon when I want to ring out a sub-E0 note.
 
In the mid 1970s Fender put out a 5 string short scale bass, tuned E - C. It was unsuccessful, but IMO they got one thing right and that was the PU orientation. (pictured below)

The lower 2 strings could be individually height adjusted, while the upper 3 were averaged.

The reverse orientation would also help tame the thump of the lower strings, and fatten up the upper strings.

I am a great believer in the reverse P, and I never needed a HPF until I used a 5ver with soapbars. I expect there will be many traditionalists who will disagree.

As your bass has a pickguard then a luthier could easily and cheaply rout the body and provide another pickguard (of your choice). If you remain unhappy with the result it would be easily returned to the original.

I say think outside the box and get youself a better, original sound. If I was starting out again I would go in this direction.
 

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There may already be a similar answer, but the easy answer is to lower the side of the pickup that sits underneath the B string. I got a P5 a few weeks ago and had the same "boom" of the lower strings, and just adjusting the pickup height seems to have mostly cured the issue.
 
Have you played some variety of other 5ers? There's hardly anything you can do past a certain point if you're banging it. I mean, if you "consistently" bang all strings the low B might "overreact" compared to other strings. I do bang my strings with a pick (soft pick, alla' Nolly -Periphery-). That requires copious amounts of compression. Mostly to tame the low B string, which many overdrive/preamps will still have a hard time taming in the first place.

I too have a heavy hand for fingerstyle (and use a cleaner sound). Over time, I've developed an automation to pluck the low B string closer to the bridge when using the neck/P pickup only. It both reduces waves' amplitude AND provides more articulation, a clearer note (VERY welcome if you're only capturing vibration at such spot). I tend to go with the balance in other combinations and don't move (except for the ocasional note I want to fatten/lighten), just do this low B displacement without thinking when going neck/P soloed, I just feel the bass asks for it. I definitely don't like playing the low B over the P pickup solo unless it's real soft, deep but soft attack. You can probably wreak havoc with the B string on any bass.

Not saying there can't be anything wrong with your bass, it clearly is when it's so noticeable to you, just sharing some extra tips, even for any properly working 5er.
 
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People around here have doctorates in compressorolgy. I don’t, but I do use a compressor last in my chain for this reason. I think it’s a DBX 166 model, the way I set it doesn’t seem to affect the tone audibly, other than reining in the B transients.
 
Have you played some variety of other 5ers? There's hardly anything you can do past a certain point if you're banging it. I mean, if you "consistently" bang all strings the low B might "overreact" compared to other strings. I do bang my strings with a pick (soft pick, alla' Nolly -Periphery-). That requires copious amounts of compression. Mostly to tame the low B string, which many overdrive/preamps will still have a hard time taming in the first place.

I too have a heavy hand for fingerstyle (and use a cleaner sound). Over time, I've developed an automation to pluck the low B string closer to the bridge when using the neck/P pickup only. It both reduces waves' amplitude AND provides more articulation, a clearer note (VERY welcome if you're only capturing vibration at such spot). I tend to go with the balance in other combinations and don't move (except for the ocasional note I want to fatten/lighten), just do this low B displacement without thinking when going neck/P soloed, I just feel the bass asks for it. I definitely don't like playing the low B over the P pickup solo unless it's real soft, deep but soft attack. You can probably wreak havoc with the B string on any bass.

Not saying there can't be anything wrong with your bass, it clearly is when it's so noticeable to you, just sharing some extra tips, even for any properly working 5er.
Yeah, i have a custom 5er that is quite different: less string spacing, neck through, more flat radius, humbucker, and is super balanced. The problem with this is the B is floppier and the other more rigid so you almost always bang the B without wanting too, is too loose
 
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There may already be a similar answer, but the easy answer is to lower the side of the pickup that sits underneath the B string. I got a P5 a few weeks ago and had the same "boom" of the lower strings, and just adjusting the pickup height seems to have mostly cured the issue.
Yeah, the problem is it decrease the E and A volume too. Thats is the problem. I can make G and B sound balanced but in the "bass coil" of the P pickup the B over powers E and A