The Theoretical Minimum lecture series on theoretical physics by Leonard Susskind. Covers the basics in a very approachable way. I wish this had been available when I studied physics.
When I was in school "scientific method" wasn’t teached as a separate topic, but more like the result of "osmosis": you are given many examples of how science works and you somehow learn by this the process of science itself. Ok, you are taught how do do proofs in maths and how to do experiments, but no direct reference to a concept like the scientific method.
An (maybe) interesting fact is, that in Germany the notion „scientific method“, to my knowledge, is largely unknown. For example, there is no link in the english wikipedia entry you have given to the german wikipedia. When I studied physics in Germany no one ever used that term.
There is a free PDF on the nature site, but the paper is also available on arxiv (https://arxiv.org/abs/1407.4437), the first version on the arxiv dates back to 2014. It's strange, but I find the arxiv version much more readable in terms of typesetting than the polished version in nature. Also there are additional appendices in the arxiv version.