The standard study of Milton's use of rhythm and meter is Robert Bridges' classic Milton's Prosody: With a Chapter on Accentual Verse and Notes. Revised Final Edition. Oxford: Clarendon, 1921. The book explains Milton's use of unrhymed iambic pentameter in Paradise Lost, including discussions of three variations:
- When a line has fewer or more than ten syllables
- When a line has fewer or more than five accented syllables
- When the feet in a line are other than regularly iambic.
The book goes on to discuss a "relaxation" in Milton's prosodic practice in Paradise Regained and Samson Agonistes, and concludes with a section on "Obsolete Mannerisms", including recession of accent, spelling, and pronunciation. The monograph is available for perusal and download at the Internet Archive.
Another useful study which builds on (and in some cases disagrees with) Bridges is Milton's Art of Prosody by S. Ernest Sprott, Oxford: Basil Blackwell, 1953. Chapter II of the study, wherein Sprott tries to deduce the general principles of Milton's prosody, would be particularly helpful for your purposes. Chapters V–VIII inclusive parallel the structure of Bridges' treatment of Paradise Lost exactly. This book can be borrowed, but not downloaded, at the Internet Archive.
Gilbert Youmans has an article on "Milton's Meter" in Phonetics and Phonology vol 1, 1989, pp. 341–379. Unfortunately the article is paywalled, but here is the link in case you wish to purchase it or have access via a library: https://doi.org/10.1016/B978-0-12-409340-9.50017-6.
John Creaser, emeritus professor of English at Oxford U, has three articles on Milton's prosody, but I'm unable to access any of them online. You may have better luck if you have access to an academic library:
- Creaser, John. “Prosodic Style and Conceptions of Liberty in Milton and Marvell.” Milton Quarterly, vol. 34, no. 1, 2000, pp. 1–13. JSTOR, http://www.jstor.org/stable/24465208.
- Creaser, John. “‘Service is Perfect Freedom’: Paradox and Prosodic Style in Paradise Lost.” The
Review of English Studies 58. 235 (2007): 268-315.
- Creaser, John. “‘Fear of Change’: Closed Minds and Open Forms in Milton.” Milton Quarterly, vol. 42, no. 3, 2008, pp. 161–82. JSTOR, http://www.jstor.org/stable/24462119.
Finally, Michael Taylor, then a student at Stanford University, wrote a senior honor's thesis, How Milton's Rhythms Work (2015), under the guidance of Professors Blair Hoxby and Roland Greene. The thesis is available for download at this link.