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What's the best modification you've made?

Brass nut. I installed it with promises of magical tone improvements, which mostly turned out to be claptrap. However, it has one very useful effect: open notes sound as strong and sustain the same as fretted notes, so I don't have to worry about finding the 5th fret when diving down to a D or A (for example).

I love it - would have either that or a zero fret on all of my fretted instruments if I could!
 
I have what started out as an SX P/J with a Jazz body. Over the last two years I have turned it into something else entirely with two SCPB-3s, a three way switch, two volumes and no tone, and the Ric-o-sound double output jacks. A couple weeks ago, I completed it's transition to being as close as possible to a Rickenbacker by installing a "vintage switch" that puts a cap in between the bridge pup and the outputs. By far the coolest mod I've ever done.
Pics please..
 
Medium scale conversion necks (Lowe Custom Guitars) on a Fender MIM Jazz, home built P bass, and medium scale conversion neck (Switzerville Guitars) on a Cort B4.

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The best single mod I recall was replacing the stock bridge on my Epiphone Allen Woody with the fully-adjustable Hipshot upgrade. It transformed the bass from so-so cool bass to a really nice player. expensice bridge, but worth it.

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Yeah, the HipShot SuperTone is a great bridge and a must-have replacement for the old Gibson three-point bridge. The Gibson SG basses have been upgraded in recent years to use a Babicz bridge that looks to be comparable to the HipShot, but Epis still seem to use the old bridge.
 
I am always amused when I hear about the Fender fans swapping out their pickups. Apparently, Leo got it right, yet the first thing many players do is swap out the Fender pickups the minute the bass arrives.

"WOW, my Fender REALLY sounds great, now that it doesn't sound like a Fender!"
~
I have made a similar observation about my Franken-Ric at times.

After the completion of all of the pickup and electronic mods which I performed during my first decade of owning it, it now sounds more like a Jazz, mainly due to the placement of the pickups and the simpler electronics of pickup selector switch, one volume, no tones, and no capacitors, though the PUs are EMGs a la Steinberger.

However, unlike a stock Ric and Jazz, there is no hum.

BTW, hum was what first prompted me to begin my many electronic mods to this 4001.
~
 
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Brass nut.

I installed it with promises of magical tone improvements, which mostly turned out to be claptrap. However, it has one very useful effect: open notes sound as strong and sustain the same as fretted notes, so I don't have to worry about finding the 5th fret when diving down to a D or A (for example).

I love it - would have either that or a zero fret on all of my fretted instruments if I could!
~
For many years I have been thinking of doing exactly that mod to my Ric, to even out the character of the open notes with the fretted ones.

I have noticed that some Hofner basses come with a 'Zero Fret'.
~
 
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Varitone, specifically the one developed by David Certain and his electronics tech. Had him install it in one of my Jazzers in addition to a standard tone pot. A couple of those varitone settings are just killer.

Hipshot Ultra light tuners on a Gibson T-Bird that has a sparkle re-fin by Marty Bell. What little neck dive it had was cured, and they are really accurate.
 
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These two MIM Fenders were nice to begin with, but with a couple tweaks they became superb basses.

Added a battery box on the back of this P bass. It has an EMGX pickup, so replacing the battery that was squeezed into the control cavity beneath the guard was a royal PITA.

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This Fender FSR Jazz had DiMarzio dual coils when I got it, didn't care for the tone at all. Replaced them with Fralin raised-pole singles which sound fantastic. Also added Gotoh Res-o-lite tuners for better balance. Swapped the greeny white guard for a tort, which as everyone knows, improves tone by a factor of ten.

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Edit: Both basses came with Hipshot "A" bridges, replaced them with Fender vintage threaded saddle bridges.
 
My 2013 MIM Precision Bass Special. Installed Babicz full contact bridge, Aguilar PJ p'ups. Had the crappy Fender preamp removed and rewired as Volume, pull up series, balance, two tone controls. Tonight ripping all the wiring out and hooking up a 4 band Audere to the Aguilar p'ups. Volume for each pickup, treble, hi mid, low mid, bass. I have great expectations. It's a great playing bass, just looking for more tone options.
 
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My 2013 MIM Precision Bass Special. Installed Babicz full contact bridge, Aguilar PJ p'ups. Had the crappy Fender preamp removed and rewired as Volume, pull up series, balance, two tone controls. Tonight ripping all the wiring out and hooking up a 4 band Audere to the Aguilar p'ups. Volume for each pickup, treble, hi mid, low mid, bass. I have great expectations. It's a great playing bass, just looking for more tone options.
In addition my 2003 MIM Fender fretless jazz now has DiMarzio Area J's and a Geddy Lee neck. This particular neck has the truss rod screw at the bottom, I used my dremel tool to cut an adjustment relief in the body. Ironically I've never needed to touch the adjustment, even after going from Chromes to SS rounds!
 
Turning both of my uprights into 5 String Basses. Dropping the low String to “D” for adding depth, and adding a High “C” for upper register sweetness. They are both truly amazing sounding for what they were originally....A Mathias Thoma hybrid, and a no name Korean Model.