What's the best modification you've made?

I put a hipshot aluminum bridge on my Am Pro P-bass V. I have always wanted a passive 5 string bass with the tone and sustain of a 4 string Am Sd p-bass. Back in 95 when they 1st came out I bought a Am Sd p-bass. It has the tone and sustain I like best. However, I prefer 5 strings as I have developed my technique over the past 20 yrs around all 5. Enter the Am Pro p-bass V. It has a split p pup in the p position. It has passive electronics and the fit and finish is great. But compared to my 95 p-bass Am Sd, the tone is darker and the sustain is much longer. This is all due to the greater mass of the Fender hi-mass bridge and the wider heavier neck. You can EQ it by cutting some lows (hi-pass) and brighten things up but, you can't EQ sustain. Longer sustain gives the bass (imo) less punch and more of a pipe organ type tone. This is great for some types of music but not what I was after. I want more of a bell tone, a drop in volume after the initial punch. Enter the Hipshot FM3 Aluminum type A bridge. It is much lighter than the Fender hi-mass and probably close to the weight of the traditional bent plate type that comes on the Am st p-bass. The sound is noticeable brighter and the sustain is a little shorter. Still not as short as the Am Std but closer.

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hipshot pb5 by TOM STRAIGHT, on Flickr
 
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Switching my PJ electronics from a VVT setup to a master volume/master tone/3-way pickup selector configuration was a very worthwhile mod for me. The elimination of the pickup loading effects of the VVT setup was like removing a blanket from in front of the speakers ... noticeably more live sounding. While I gave up tonal options by not being able to mix the two pickups any which way, the fewer tones available to me were better ones, IMHO.
 
Adding Lindy Fralin's hum-canceling Split-Jazz pickups to my 2003 MIA Fender. Eliminated all the single coil hum, and if anything improved the tone. I've tried five sets of noiseless J-bass pickups across three different basses, and the others were all good in their own way, but IMO these are the best for preserving classic J-bass tone. They have lots of punch, and growl for days. I've had them for 13 years, and they're staying in this bass for the duration.

Yep, the Fralin Split-Coils are great for J-basses. I would be interested to try Zexcoil's J-bass pickups, too, because I love their Strat pickups, but I bought the Fralins before the Zexcoils were available and I haven't had a need for more J-bass pickups.
 
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Stacked knobs. I think every bass should have them.

I won't say it resulted in a great improvement in tone by itself,
but being able to control both volume and tone individually with dual pickups,
results in more variety of tone.
 
Rewirings - I've done dozens on my basses (and for others), and the tonal control you can have doing that (assuming you know what you're doing) is pretty spectacular.

In terms of physical changes, putting an ebonol fingerboard fretless neck on a bsss changes its tone quite a bit. Kinda messed with intonation, though...;-)
 
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I may be in the middle of it now.

I've a Hofner Icon violin bass with a damaged body for several years and finally decided to to something with it.

I always wanted a solidbody with an Icon/Ignition sized neck (more narrow than the Contemporary and German versions) so last weekend, as a proof of concept exercise, I sawed the violin body and mounting block off of the neck and did a quick install of the neck on an Epiphone Les Paul Special II bolt on guitar body.

The neck pocket is 7/64" too wide on each side of the neck but it doesn't seem to hurt anything. I used an old Wilkinson 5 string 3D bridge with just 4 of the bridges to handle the narrow string spacing. I kept the stock humbucking guitar pickups and controls of the Epiphone. I was surprised how good it sounds. I've been using it for a few days and it will be going to rehearsal with me tonight.