You've got a bunch of good suggestions here, but I have one more hypothesis. Check to see if your
truss rod cover goes under the back edge of your
locking nut (or if there is anything that might be in contact with the nut). On my S370 the truss rod cover was underneath part of the locking nut and it made the cracking noise you describe. I got the creaking whenever I tightened and untightened the pads or when I used the trem. I trimmed the truss rod cover and the cracking went away
