The replaced frets are dominantly responsible for this. When you re-fret a guitar neck, especially one with vintage style trussrod (compression type), you change its mechanical and vibrational behaviour: resonances will be shifted and their Q-factors will have other values as well. Replacing tuners can have a similar effect, if they're not the same exact mass than the original the low order bending (and torsion) resonances might change. Neck resonances "pull off" energy from the vibrations, that's why they have huge impact on tone.
IME "good" guitars have necks with lot's of low damping (high-Q) but well distributed resonances which just happen to not be exited (or least only very little and well balanced accross the fretboard) because the notes on the neck that have those specific resonance frequency also happen to appear were the vibrational pattern has a null/minimum and thus cannot be exited much. Preferably the peak frequencies should lie in between a semitone interval (a quartertone off).
Removing the dirt doesn't change anything (well, maybe the strings may age now less fast) unless you have soaked the fretboard with whatever detergent and/or fretboard oil used.