For fret noise, the main question is:
Is it my technique or is it my instrument setup?
Turn up the volume, cleanly fret a note (right on top or just behind the fret), and pluck lightly.
Keep your fretting hand in place after plucking. Do this in several places on the neck.
If if buzzes while let ring the cleanly fretted note, it is likely to be a instrument setup issue.
Which could be string height OR neck bow/truss rod.
(since it only happens on your E string, I'd suggest raising the E string up first)
If it only buzzes when you are playing phrases and riffs, it is likely to be a technique issue, generally lifting your fingers off the string too slowly.
I posted an exercise for clean fretting in
this thread
As mentioned, there is always a minimum amount of squeak and fret noise with rounds and an open tone knob,
My experience is it gets lost in the mix.
