Folks, having been there/done that with putting different necks on the same body.... necks made of differente woods, or the same wood with different fretboard material, I can tell ya....
Ruling out the player.... and the amp (because the amp is half of the tone at least, and an instrument in itself)
#1 - its the pickups stupid
#2 - neck wood and contour. I dont thing maple vs ebony vs rosewood vs goncalo vs pau ferro makes a difference on an otherwise very stiff neck - like maple. On a mahogany neck or other neck with some wood less dense than maple, less stiff than maple, then there is probably some effect.
#3 - how you wire it
#4 - strings
#5 - everything else in a very distant last place. Finish - nil effect on a solid body. Bridge, almost nil, nut almost nil, fret material, just over almost nil. Certainly there is more effect in tone with changing string type (ie pure nickle vs plated, vs stainless) than in fret material.