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Question about intonation

This is hard to explain, when I play the A string on the 7th fret and up, I hear a metal tin noise, sounds like to pieces of metal crashing into each other, or a high frequency whistle yet the note is still pronounced, I hear it once I am plugged in. Any idea what is wrong?

It sounds like the A is making slight contact with frets higher on the neck than the note you're fretting. If you measure the gap between the neck and the bottom of all the strings at around the 20th fret and the A is less, adjust the saddle higher on the A. If all four strings are the same, loosen the truss rod by a quarter turn or so that the strings make the neck bow a little bit more. Those are pretty much the only two variables you could be dealing with................................
 
Springs on the bridge can vibrate and make noise as well. Also the truss can vibrate, this is unusual, but can happen. Slight adjustment will usually fix it.

You're gonna have to really isolate each and every part starting with the most obvious.

Mechanically - the strings (of course, since they are supposed to vibrate) then the upper nut, saddled, (I'd forget about the springs on the adjuster screws for now), the bow of the neck and resulting string noise, high fret, a twisted string can cause some oddball harmonics; then perhaps it's an anomaly in the electrical circuit.

It could also be the output jack just messing with ya too or a slightly loose wire connex inside the pickups or pots - maybe even a partially shorted cap. Grabbing at straws here.

Go simple-to-complicated.

When you hear hoofbeats, don't get froggy and assume zebras at the start.