Success~

The string height at the 12 fret was .110, so I lowered the bridge to .080, and widened the nut slots for the heavier gauge strings.

The intonation is much better than before, though I seem to be out of intonation adjustment room on the bridge and a few strings are still not sounding ...

Thanks for the informative replies, it's good to hear others are having good results with even larger strings.

I'll work on these ideas tomorrow morning.
The nut slot issue seems a good place to start.
As mentioned, the strings are likely riding high in the slots, and that seems to fit the symptoms ...

I’m having intonation issues with my classic. As an acoustic player with a heavy hand I’m probably asking a bit much but I do want to try because I love the Fly, feel, touch, and sound.

Strings are 11-52, tuned to Eb. Same as on my acoustics.

Original set up carried a #9 spring which I switched ...