In method addPMID() in the file lib/zotero.js, currently the PMID is extracted from the extra field in the citation object. However, the PMID is only found in the extra field when the metadata is being extracted from a link directly from http://www.ncbi.nlm.nih.gov/, but not if a different URL to the paper is used, such as one on the publisher's website. If a citation object contains a DOI (citation.DOI), you can use the DOI to look up the PMID and add that to the citation using the PubMed API: http://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/ If there is no citation.DOI field, you should not do anything as the source either does not have a PMID or if it does, would be very difficult to find without the DOI.
Hint: use the "request" library: https://www.npmjs.org/package/request
Hint: JSON is a great format to use in conjunction with Javascript because it is very Javascript object-like!
Bonus points: Add the other IDs available from the PubMed API to to the citation object. You should think about how the code should be structured in order to avoid making more than one request for the same information.