I saw a question on here by Jerry Gibson regarding surface pickup too high and thought I would explain the problem and the possible solution.
The issue is I suspect that the bridge is too low, the action may be correct as that applies to string height over the fingerboard.
The remedy is to raise the bridge to get the clearance needed, then adjust the neck angle to get the desired string action over the fingerboard.
Or instead of angelling the neck, raise it so it is higher above the surface of the top. this will also give a better break angle off the back of the bridge.
Hope this helps. Taff
On the topic of Flatpup’s, I like to build mine with the fretboard positioned 1/4” above the box. Flatpup’s are 1/4” tall, so the strings will have enough clearance to still have a somewhat lower action, granted the bridge is tall enough like you said Taff? Good luck mr. Jerry