I'm about to make the 100% leaderboard less empty, but I need some clarification on timing. Assuming I do Fishing Net Bonus last, should the clock stop when the last Pebble drops, or when the save prompt appears on the Level Select?

Timing ends whenever you finish the level where you collect the final star, when the screen fades to black. I think that makes the most sense. One thing that should be checked though is that if you can collect a star and then quite out the level, does it still count the star?

From experience, the Star does count if you quit after collecting it. However, this isn't useful in 100% outside of backtracking, since you need to finish every level anyway, and I'm pretty sure finishing FNR is required.

ok. If that is the case, timing will end whenever you quit out of the level with the final star, whether that’s through finishing a level or quitting out of it from the pause screen.