The leaderboard says to stop after the credits stop rolling (which is strange, since you can actually skip the credits), but the guide says that the timer stop once all the students initiate the shutdown sequence. Which one do I use?

The timing rules were changed to mirror what danganronpa 1 does which is why the guide says to stop the timer at the shutdown sequence since that was the original timing. So you would stop it when the credits start rolling after the epilogue. If you want an example of the timing, refer to kaamosteoria's mean run on the leaderboards.

Okay. Thank you!! :)