1) If you still have the fret board, measure that, and measure how proud the current neck sits above the surrounding wood. Add those two numbers together, and subtract them from the thickness of the bolt on neck. That will give you your pocket depth.
2) If the neck is already finished, don't worry about it. You can always mask off the neck pocket before finishing. There is no need to paint the neck pocket.
3) Most likely a flat pocket will be fine, if you happen to have trouble you can always shim the neck. With the way that bridge is recessed, I would guess that there isn't very much if any neck angle.
Great stuff. I do have the fretboard pieces so that math will be easy. I may factor a bit less depth just to compensate for the fretless fingerboard ending up at what the frt height was. Thank you!