Your article is too long to address every piece of evidence in this format where we are limited to 30,000 characters.
But there are problems even between the article and the evidence. For example, in the section on Randomized Controlled Trials on Wheat, you say:
This advice resulted on a 22% death increase:
However this result bordered on statistical significance: the 95% confidence interval being 0.99–1.65.
Had the study last a little longer, it would have raised way more suspicion toward whole-grains.
However the abstract of the linked study says:
Subjects given fibre advice had a slightly higher mortality than other subjects (not significant).
When a result is not significant, it is not significant. We can't use an insignificant result to make the claim that the "advice resulted on a 22% death increase". We also can't say that it "bordered on statistical significance" without further evidence that it actually did. We certainly can't predict the future outcome of a trial without actually conducting the trial. If we could, we would be even have trials?
A couple of paragraphs from Reflections on the Diet and Reinfarction Trial (DART) illustrate some of the problems with trials of this sort that lead to insignificant data. In the past, fibre has been seen as having a protective effect rather than the detrimental effect your article is claiming.
The relationship between fibre intake and mortality was paradoxical: within the group advised to eat more fibre there was an inverse relationship between fibre intake and mortality,yet its overall mortality was higher than that of the group not given this advice. There was a favourable effect of compliance with all three interventions, of
roughly equal size — a ‘healthy complier effect’ that was independent of the efficacy of the intervention. Good compliance seems to be a marker for something else, possibly a tendency to comply with other aspects of management that really do bestow benefit, or perhaps a better state of health: conceivably, people who feel unwell cannot be bothered to follow uncongenial diets. It is very difficult to allow adequately for such confounders.
These findings illustrate the importance of the controlled trial as against observational studies. If the subjects advised to eat fibre are treated as a cohort, they appear to provide evidence of a protective effect of cereal fibre, an impression which the randomized trial shows to be misleading. Several cohort studies have shown an apparently favourable effect of cereal fibre on CHD[8–11], but confirmation by a randomized controlled trial is lacking.
Directly after your claim that the trial would have found statistically significant results if it had lasted longer, you make the claim:
In fact, researchers found this effect to be statistically significant in a follow-up study.
However in the abstract of the linked study:
Fat and fibre advice had no clear effect on coronary or all-cause mortality.
You claim is contrary to the abstract of the paper.
It's worth noting that the fish results changed in the follow up paper as well.
The early reduction in all-cause mortality observed in those given fish advice (unadjusted hazard 0.70 (95% CI 0.54, 0.92)) was followed by an increased risk over the next 3 y (unadjusted hazard 1.31 (95% CI 1.01, 1.70).
In the following sentence, you state:
After adjusting for pre-existing conditions and medication use, we can see in the table 4 of this study an hazard ratio of 1.35 (95% CI 1.02, 1.80) for the 2-year period of the randomized controlled trial.
This is a case of cherry picking. You have chosen the highest number on the page, regardless of its relevance and failed to mention that in the same group in following years the ratio was reversed. More people who were not given the advice died than those who were given it in some time periods.
The paper includes comments on this table:
All-cause mortality was increased in those given fibre advice in the first two time periods but reduced in the later time periods such that there was no long-term effect on survival. A similar pattern was present for coronary death. The risk of stroke death was slightly increased.
While I haven't addressed every claim and every paper your article contains, the small part I did examine shows that your article does not do a good job of correctly reporting the results of the studies.