For retiming runs, what is the correct starting frame? I was guessing it's the frame when the koopa's stop moving, but it seems like they continue moving a bit after the Start button is pressed.

Scroll to the bottom here: https://docs.google.com/document/d/1gVoljNjR3lagg9EgqONeQZ9FQVhtBEz5mkyPdmpXZy4/edit#heading=h.m9yf2rct9jp4 there's a distinctive image with about 15% of the curtain up top with tan lower 85% or so. That frame is 54 frames after start at 60fps. More detail is in the doc.

Thanks for the tips. From what I'm reading around here, it sounds like it would actually be preferable to leave milliseconds off of submissions? I've gotten in the habit of frame counting all of my PB runs, and fixing my splits just for my own sake. It looks like there are some good resources in that doc. I've been using avidemux, but it seems like there are some more purposeful tools linked to in there.

preferable to leave milliseconds off of submissions

Yep! Mods will delete milliseconds anyways in most cases. It should save you some time to get more practice+attempts in too :)