I finally had a successful attempt today on what must've been my 10th run. I've spent an embarrassing amount of hours and repeated attempts to get this. I'm in CH3 so it's definitely possible to do this before later in the story.
My successful run was seemingly no different from any of my previous runs, I really don't have any advice for others trying to do this other than cross your fingers and hope whatever ****ed up algorithm they have for this challenge counts your run.
I think the puddles that appear in the train tracks count as water if you run in them, same as the puddles that are in the ground at Van Horn... but I've seen videos of people running right through those puddles and it still counting so I have no idea anymore. Just to be safe I'd avoid all water, no matter what. Take the time to go around puddles no matter how small, that's the only thing I can think of that ****s over otherwise smooth runs.