I am pulling my thesis together, with 4 published chapters. The university says published papers should be included within the document, maintaining the formatting as they have been published. I have figured out how to do this two ways:

1) Convert the PDF to a Word document. This is much cleaner to read, but the sizing can be tricky to format into an A4 and, more critically, I have found that with at least one of my papers it messes up the scientific notations (They are basically free-floating around in the paper rather than staying within the sentence structure.)

2) Save each page of the article as its own PDF and then insert it into the Word document as an object, page by page. This is easier in terms of spacing and pagination, however the quality of the formatting is poor - it looks very fuzzy. I am worried when I convert it back to a PDF as a full document it will be even harder to read.

I have looked at other theses and their inserted papers look very clean and crisp. Does anyone have practical tips on how to maintain the quality and the formatting at the same time?

Yes. Use Latex!

First I would double-check what the mean my maintaining format- for my uni that just meant keeping the same heading and information etc
So I added in the word document that I would have sent to the journal for review -I didn't put in with two columns etc- I did change the referencing to match and on the title page foe reach chapter I wrote this paper title XXXX was published in XXX and gave the DOI and author list plus contributions.

The other option would be to save up as far as the first paper as a pdf, your pdf paper, then the next part as a pdf and merge all pdfs together or alternative leave blank pages for the pdf in word, print your thesis- on the pages for the pdf print the pdf on these pages, but the document back together and scan the completed version.

Thank you; those are very practical and helpful suggestions. I hadn't actually considered pulling the whole thing together as discrete PDF's which I think may work better all around, so I will experiment with that option first and go from there.

Eek! I think it's too late for that clever solution but maybe it will help some other poor soul.

I thought I should post how I resolved this problem. I paid for an upgrade to Adobe (DC), which allows one to combine multiple PDF files. I convert my Word (unpublished) chapters to a PDF, drag all the discrete pieces together in the order that I want them, and then combine into one document. This also allows me to remove the pages (or sections of pages) with references and add in a full reference section at the end of the document, as well as include natural pagination for the entire document.

I would suggest using apa article citation while formatting your research.

Firstly, I would advise you to use the APA Citation style in your work, which will make it easier for you, because most of the universities in the world use it and it is quite easy to understand. Different citation rules apply to articles, books, and other sources, so I recommend that you check the source before creating a citation. Visit https://edubirdie.com/citation/apa/cite-an-article/ for detailed information as well as a citation generator to help you automate your research writing process.