I will lay out here the starting points you should use for NFM speedrunning. The reasoning behind these decisions will be spoiler'd below for your convenience.

Full-game: Right when you skip the camera panorama of the stage, you should start your timer. In other words, the first frame of "3" on the countdown. [spoiler]Since a key needs to be pressed to skip the panorama anyway, it is easy to press your split start key at the exact same time, allowing for an extremely precise starting point that will not vary between runners[/spoiler]

Level Leaderboard: Start your timer right when the countdown says "Go!" [spoiler]Individual levels have shorter end times than the full-game runs. The Introductory Stage run is less than a minute; therefore, including the 3-second countdown in the time does not make much sense. There will be slight variation between runs, but if everyone makes an effort to start as soon as they see "Go," there should be no problems.[/spoiler]