How to explain my methods and results? I currently am writing a paper which uses regressions (from statistics) heavily. The objective is to show (as far as possible) that A causes B.

The main analysis of my paper uses regressions to show that A is correlated with B. 

After showing this correlation, I wish to show that A occurs before B occurs so as to give further evidence of a causal relationship. This requires another set of regressions. (The set of explanatory variables changes significantly, so I need to specify the new regression equation.)

Furthermore, I need to show that factors C, D, E mediate the relationship between A and B. (Again, I am much better off specifying the new regression equation. Even if you doubt this, just believe me on this)

How should I go about this?

Option 1: Explain all methods (correlation, temporal precedence, mediation) in the Methods section. Then give all results in the Results section.

Option 2: Explain the methodology for detecting correlation, then give the results. Then explain the methodology for temporal precedence, give the results. Then explain the methodology for mediation, and give the results.

The problem is, no matter which way I do this, I get criticism that the structure is confusing, along with suggestions that I should do the alternative approach. For example, if I try option 1, people say that temporal precedence and mediation only make sense if I detect a correlation, so these analyses should be shifted to the back. On the other hand, if I try option 2, people say that my methodology should all be neatly encompassed in a single Methods section.

I'm curious as to what most people do when they are in a similar situation?
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.