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What's the best modification you've made?

Best improvement I made was to go to a short scale...it fit me better and made switching to and from regular guitar easier. I have kept my Fender Mustang bass. The only long scale bass I kept was an acoustic Martin. Hard to find a short scale acoustic bass.

I've often thought of trying different PUs on the Fender but can't seem to gain the motivation to try it. I've experimented with acoustic PUs on guitars but I'm more familiar with improvements that can be made with that technology. I wouldn't know where to start with the Mustang Bass.
 
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Ha! I did this same thing with the BA bridge on my 60s jazz. I bought it used where someone had stuck a BA bridge on it and the strings not passing directly between the poles on the pickups set off my OCD. I bought a 60s threaded bridge, swapped them out and have been very happy with tones. I really think it was the string spacing.
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On my FrankenRic, I put grooves in my BAII bridge where I wanted them, not only for the where the strings would sit over the pickups, but for they sat over the fingerboard.

When I got the EMGs, I could not see pole pieces any more, and the bridge was already set as above, so I positioned the pickups where I wanted them, and all was fine.
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My MIM P-bass got a set of QPs to replace the stock pickups, and a reissued Fender Wide Range Humbucker in the neck position, Billy Sheehan style.

Holy crap.

This bass has tone that is heavy, grindy, and aggressive as hell. Lots of people say the QPs scoops out too many mids, but the WRHB adds back those muddy low mids by the bucketload, and puts out low end like you wouldn’t believe.

I configured for wiring to be exactly like that of a ‘60/61 Jazz Bass, two stacked independent volume/tone knobs. I love the way I can make the tone pots interact, the shaping capabilities are endless! I’ll take a picture when I get home tonight
 
A bridge or upgrading the electronics...

The first Jazz bass I owned was an old Squier, probably an Affinity. I got it off of Ebay for $75 shipped from some pawn shop. Over time I added a Gotoh clone bridge which really helped the sustain, and then eventually put an Audere pre in it that sent it over the edge. It's a nice bass now.

The first thing I usually seem to upgrade is the bridge. That seems to have an effect on several aspects of the bass.

BnB
 
Installing a second battery into my Euro Spector that had an EMG BTS preamp, there by converting to an 18 volt system. Super increase in headroom and allowed punch in tone.

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Excluding strings, what's the best modification you've made to a bass guitar that resulted in an improvement to the sound?
It may have been an improvement to the sound per se however it did make it easier to play. I added the Zero-Mod thumb rest to my Rickenbacker and it is wayy more comfortable to play. i also added one to my Ernie Ball Music Man Stringray and it allows me to move where I pluck the strings to the nech or over the pick up or in the middle and that way actually gives me different tones. And the basses remain un toched as it is only a screw on attachment using the same holes.
 
new pickups (Dimarzios) and Gotoh bridge for my Jbass and (Seymour Duncs) for the Pbass and changed the neck from maple to lefty rosewood and new wiring.
 

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Best modification I made was to properly shield the control cavity on my 2000 Warwick Thumb NT4 and to replace the two op-amp integrated circuits with quieter ones.

Before the mods, in certain studios (near radio transmitters, I heard lots and lots of radio interference. And the hiss from the bass's pre-amp was objectionble to me. Now, there's no radio interference and the his levels are much lower and more acceptable.

As it came from the factory, the black paint in the control cavity was not conductive. That means that it was not doing anything to shield the electronics. Also, the control cavity cover was made of plastic and also not shielded in any way.

The original two op-amps were optimized for long battery life, and not quietness. I'm willing to live with shorter battery life in exchange for much less hiss.