Hi @varshilmehta,
Very good! You mostly caught the concept. First of all, references were not parsed as requires. Reference section must be named as References (in lower case) not REFERENCES. You can see this part of code here: DOCX2JATS/transformerBiblAMA.java at master · Vitaliy-1/DOCX2JATS · GitHub
[Rr]eference means that the program will catch the word, which starts with the first letter R or r (might be in lower or upper case), and eference must be only in lower case. Letter s is optional.
I can make this part of code case insensitive in the future release.
After simple renaming converter will parse them as requires for JATS standard.
Secondly, the older Lens Viewer version, that is used by default in OJS3, is not really for public use. It checks the publisher name in the JATS XML and if it is not a eLife Sciences it blocks the transformation. So you need to update Lens Viewer to the newest version. It is really not hard. Take a look at this topic: Can't view XML file in OJS 3.0 - #30 by Vitaliy
Let me know if you will encounter with problems.