Well I hate to hear this, but putting it aside for a bit may be the best thing. There were a number of things suggested that I am not sure you checked. As an example, rockering frets. I don't care how high your action is, if you have a high fret, that can only be realized by measuring against adjacent frets. Action doesn't come into play on this.
Also, you never truly checked for string impedence other than eyeballing it.