Issues when splitting one long paper into two papers I've got a long policy/economics paper that will need to be split into two papers before any journal will be able to publish it.  I can make them into freestanding pieces.  But there will be significant overlap, particularly in the introduction, data description, and methods.  

Is it frowned upon to have entire paragraphs be identical between two papers?  Structure will be something like the following:

Introduction
    Para A1
    Para A2
Methods/Data
    Para B1
    Para B2


and for the other

    Introduction
        Para A3
        Para A2
    Methods/Data
        Para A3
        Para B2


In addition, some of the plots will probably appear in both papers. Will this be viewed as a problem?
Yes, it can be problematic if content is repeated verbatim in different sources, as it can be viewed as "self-plagiarism." The excellent Retraction Watch blog has an article that outlines the Committee on Publication Ethics's (COPE) views on the subject of when self-plagiarism merits retraction. In their proposal, the kind of reuse you're talking about could easily be considered plagiarism, even if it were cited as a quotation of the other paper.

The reuse of plots is also problematic—you'd need to make sure that reuse is allowed by the publisher of the article which appears (or which is accepted) first. If not, you can get yourself into trouble in that way as well. (Ultimately, this is how the fraud in the Jan-Hendrik Schön scandal was finally exposed.