Thesis by publication.
Ch. 3, 4 - published articles published by Elsevier permitted. Elsevier has a policy of allowing published articles to remain in theses.  https://www.elsevier.com/about/policies/copyright/permissions (click on Can I include/use my article in my thesis/dissertation).
Ch. 5 - pubished article  permitted. Has a CC BY 4.0 licence
Ch. 2B - not submitted at time of submitting thesis. Not published. Left in as stipulated by current procedure.
Ch.6. Not yet published. Left in as per current procedures. Listed as under review with an Elsevier journal. Elsevier has a policy of allowing published articles to remain in theses.