I put, a few years ago, a Fender Custom Shop 69 set in my strato. CS69´s are a vintage low gain pups, to compense this I put all pups higher that I can.
The results sounds great till 10th fret, at this point to the end of scale, in all strings, when played sounds the main note and a ghost note, like a bad octave was conected to the guitar. I disassembly the guitar about 4 times, leveling the frets twice, remake the eletrical conections one time and nothing change: the ghost note was always there. And may clearance gone to hell, this ghost note dirt completly the sound.
When I decide to remove the pups I begin to down then, thinking "this not gona happen" so I plug the guitar with pups completly down and for my surprise the sound was perfectly! The final setup was made with the neck position completly down, the middle a little bit higher and the bridge position completly high.
Well all this to ask you if you don´t try do drop the neck position pup. In my case the alnico magnets was to strong that causes this deformation in the sound.
Lucky!