Is it allowed to re-format a post-print version of a published paper? I am finishing up my thesis which will include, among other things, a published paper. I am allowed by the journal to use a post-print version, which (if I understand correctly) is the accepted version of the paper without the journal's formatting and typesetting.

Am I allowed to redo the typesetting of this version? 

The last version submitted to the journal includes line numbers and a different font to the rest of my chapters. I would like things to look consistent throughout the book. These are the instructions from the journal:

Regarding your own version of the refereed post-print only, you are free to:


post it on your personal or institutional web site and load it onto
an institutional or not-for-profit repository once accepted for
publication (access to the full text on a repository will be
embargoed for 12 months from first publication of the published
version);
use it in printed compilations of your work subsequent to
publication; and   
expand it into book-length form, and/or otherwise re-use portions in
other works.
Since you obtained the permission for the journal to use a post-print version of the paper, you should be allowed to do that.

Technically, you have two options (depending also on the thesis requirements of your department/university):


add PDF pages to your thesis (which will look inconsistent with the rest of the thesis - and you are not interested in this option)
reprint using the thesis style


In the latter case, you might do the following to the page with your Chapter title (I would also make the chapter title = Paper title, but I don't think it's mandatory):

Chapter N

Chapter Title

@2000 Publisher. Reprinted with permission (Mar 15, 2003), from J. Doe, Paper Title, Journal Title, January 2000. DOI: XX.XXXX.XXX

Page break, followed by the reprint of the journal paper with thesis formatting. 

Notice, it is explicitly stated who holds the copyright (Publisher or Journal) and that this chapter is a reprint with a permission obtained at a certain date (you might want to hold either to the email from the publisher or screenshot with the permissions).

That is exactly how I added my already published papers (2 IEEE conferences and 1 IEEE journal) to my thesis according to IEEE permission.