How much modification in a manuscript is recommended after a major revision? I've got three months to revise my manuscript I submitted to a journal a few months ago. I received two highly detailed reviews, from which it seems that the manuscript does not show the desired big picture of my work. Both reviewers pointed out similar deficiencies, and I must say, both of them are right.

According to the questions, remarks and advices, I rethought the entire paper and started to rewrite it (being attentive to the reviews), however, I am not sure if it is acceptable to completely modify the whole manuscript. Obviously, the background, the results, the theories and everything concerning the main content would remain the same with slight modifications, but I think the restructuring of the content and even a completely rewritten introduction would be necessary.

So my question is:

How much modification is acceptable after a moderate/major revision and after the decision of rejected with the chance of resubmission?
As corey979 mentioned in the comments, major may really not be major at all, and it depends on the journal. Either way, when I received review with major revisions I did not entirely rewrite the article, but addressed the concerns that the referees made. A poor rule of thumb I originally was told was to make one change per comment and resubmit.

The take away is that you should now evaluate your work having received feedback. If the edits are indeed minor (spelling, word order, grammatical) fix those and move on. If the major reviews are needed because of missing information that you have or can easily obtain you can add it as supplemental in order to preserve the original article.

If the general problem isn't framed well then maybe rewrite just a paragraph or two of the Introduction and the Conclusions. Often you can make the big picture more transparent with just a few changes to these sections. 

It is acceptable to change figure order and sections, but I would caution from departing too far from the original. If it was sent back for revisions then revise, if it was rejected then you may consider rewriting. Remember that you are telling a story, and the ideas need to flow as such.