By Aditya Shukla - creator of the brain-based guitar method
The material and gauge of your strings.
The height of your pickup, the electrical arrangement, the pots, the wiring, and the engineering.
The material and size of your pick and where you pick on the length of the string.
The Nut and Saddle break the strings vibrations, but some still remain that rebound on the bridge, which changes the tone.
While totally oversold, the guitar's wood affects how your fingers move and what frequencies get absorbed. But they contribute very little.
The cables, the insulation, the tolerance in manufacturing, the wear and tear, etc. It's not much, but is evident.
Action is for playabiliity, so your action affects your fingers pressure, which then changes the tone.
No cap. Fingers - how they touch the guitar, the pressure, the stickiness, the sound absorption, the muting, release and landing, micromovements, etc.