As far as I'm concerned, turning the volume and tone knob don't change the tone of the guitar. Any position you turn the knob to is just part of the tone of the guitar. Flipping the switch from neck to bridge isn't changing the guitar, it's just using a different setting on the guitar. Turning down the tone knob is just using another tone that was already available, it doesn't change the tone of the guitar.
Also, phrasing, timing, vibrato, the notes you choose--that's just playing. That's not the tone of the guitar, and shouldn't be confused for it.
And the choice of amp, speaker, and the position you turn knobs on the amp--is all tone of the amp, not the guitar. Guitar cables, pedalboard and effects are also not the tone of the guitar.
The things that change the tone on the guitar are pickup height, choice of strings, the saddles & nut, the choice of pots, caps, and pickups, the physical construction (body, neck, shape etc) and the physical setup. Without a soldering iron you're limited to saddles, strings, the nut, tuners, and physical setup.
If your setup sucks, the guitar is unplayable and the tone will be effected. A buzzing fret is immediately audibly noticeable, and that's a sound you might choose to play some day. But IMO playability does not equal tone.
Within this limited definition of the guitar's tone, the thing that makes the biggest difference IMO is the strings. Thomastick-Infeld flatwound chrome 13s are about as far as you can get from steel-wound .008s, and the difference is...it's a lot. And if you are not limited by magnetic pickups you get into phosphor bronze and 80/20 vs nickel vs. nps vs. NYLON. The string is where tone starts, and variations in the string can make big variations in the tone.
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