All finished, I got my Ernie balls and sanded down the top of the nut to match the string heights.
It sounds way better, the saddle changes show how much more consistent the good strings are, and more harmonics come through and overall the strings are louder. The tone pot actually does a little bit, although I still think I'll up the caps.
The extra treble is letting you hear what the cap is doing, but it does sound like it's a bit too far up the frequency range to be useful as a tone control. I'd try 0.022uF.