How much modification in a manuscript is recommended after a major revision?
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.