Would the timing for In-Level runs start upon hitting go? And then presumably end when you touch the final kelp seed of the level?

Correct. I just typed in those rules, as I must've forgotten to add them earlier. Also, I'm not thinking about adding a separate IL category for no junior helper, as you're already given unlimited lives when you do levels in replay mode.

That sounds reasonable. I'm not really sure how seriously I wanna take this game, just thought it'd be fun to relive, and IL categories seem to me to be a short but easy way to practice full runs.

And do you use arrow key inputs or mouse clicks?

Arrow keys. There's a ton more control over Freddi that way.

I'm actually going to change the rules to the time ending to when the screen either fades to black or returns to the main menu, because I've come to realize that there's a couple frames between collecting the last kelp seed and when the level actually ends.

I'd say that's a good choice, I feel as if the anticipation has me myself jumping the gun sometimes, but that's just me.