strat elite

I picked up a strat elite years ago. (I think they were only built in 84..85)
it hummed like a #@$%%$#@.....I had the pick ups changed to Lace Sensors and put in 3 toggle switchs and recently took the tone control off the middle PU and put it on the lead PU.
but the most noticable tone change was when I stripped the neck.
I hate the way the finish on the maple necks does'nt allow my hand to slide up and down the neck. (I do that a lot.)
so I took off the neck and stripped it.
when I put back on the sound was COMPLETELY DIFFERENT.
strange........could be just the way it was screwed back on....or the finish really makes that much difference????
having said all that. this guitar is a sound machine ...the switches allow you to go places regular strats don't go. the tone contols kill that ice pick to the brain lead sound. and you can get any sound you want. its great ...yes I know I destroyed any re-sale value. but I'm a player not a week end collector. no I can't put up pictures..I'm not smart enough to do that.
Question is:::: what changed the sound so much???? jmb