How to explain my methods and results?

In my area the standard is always to have a single methods section; journals would not accept an alternative format. That might not always be the ideal arrangement for every paper, but it's simply the norm.

So what to do when the methodology is somewhat convoluted, or very key to particular elements of the results? Add some "reminder" description of the methods in the results. Keep the fine details only in the methods, but address what you are up to to keep a good story in the results. Minor repetition isn't a problem and helps your paper flow.

Begin telling the reader what you intend to do at a high level before diving into the details. This gives the reader a framework for how to think about your paper.

Then I would go with option 1. Describe all your methods first. Then describe all your results. IMO interleaving your methods and results makes things confusing.

For example, readers seeking to understand your work may not care about your results, and only care about your methods.

Option 1 is probably a safer bet, because that's the logical structure of an article and it's there for a reason (to ease reading).

When faced with the same problem, I made a schematic representation of the analyses. I confronted this schema (and its improved versions) with colleagues that did not know the details of my analyses. This solution might not apply to you, but at least try. The old saying (an image is worth a thousand words) is applicable to scientific articles.