So I took a good look at the fretboard today. The CA has really helped the feel of the board, but there are still some larger cracks and holes (mostly around the nut) that the thin CA didn't help. I think I will try filling them with more viscous CA tomorrow. The whole board could probably do with a second application of thin CA, as I think I have oversanded in some places. And the frets still have scratches in them as I was much more focused on the board itself. I don't want to sand the board any more though, so when I get to the frets I will mask again so I can finish the frets without worrying about the board.

Ah, engineered rosewood, I am sure you seemed like a good idea at the time to someone...