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I made the custom bibliography using latex makebst that gives output as desired

Vergara-Buenaventura, A. and Castro-Ruiz, C. (2020). Use of mouthwashes
against covid-19 in dentistry. British Journal of Oral and Maxillofacial
Surgery 58:924–927.

I want to add period after the name of journal. How ...

I want to change the page numbers from top to bottom of the page in Master/Doctoral Thesis template. How I can do that

You have to run BibTeX on each .aux file individually. If you're using BibLaTeX, then you might need to use biber instead of bibtex, but either way: you have to process the .aux file for each chapter.

I don't know how to do that. My Chapter folder contains all the .tex ,.aux and BBL files and ...

I have compiled my thesis using Masters/Doctoral Thesis (Class File Version 1.6 (27/8/17) downloaded from:
http://www.LaTeXTemplates.com) and everything is fine including bibliography with biblatex.

But I have created a custom bibliography style file (newstyle.bst) using makebst in cmd. when I ...