What does "After working on the nut the guitar was pinging all over the place when i adjusted the tuning pegs again not a good sign." Mean?
The reason why you might be playing out of tune on a guitar that was refretted is because now that the frets are taller you are not pressing up against the fretboard wood and hence bending the strings out of tune.
The only reason why a new fret job would cause intonation issues is if the frets are not crowned well but you stated that the fret job was done well.
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