It could be coming from the neck... things to check
First loosen the strings and make sure that the neck screws (bolts in guitar terminology) are tight. Do not over tighten and make sure you use the proper size screwdrive so the screw heads don't strip. This is one place that could pop and creak.
Second the noise could be completely isolated from the truss rod adjustment - wound strings can pop if the nut slot is too small or tight - filing the nut should be done by someone with repair\setup experience as it cannot be reversed if cut to large or deep.
Note: I just saw your comment about the superglue in the nut slots... (after posting)
Truss rod, it's highly unlikely that even if the nut is stripped that the truss rod would repeatedly make noise - tuning a guitar is normally small increments (unless you are going between open tunings which require considerable tuning changes).
The truss channel is either under the fretboard (primarily Rosewood fretboards) or through the back (Skunk stripe) primarily on solid maple necks. If the truss rod has separated the neck it could creak - it should be visible from the side or back of the neck.
Hope this helps and good luck... you may need to have a tech or luthier look at it.