I'm sourcing the text (in the right hand column) from CCEL online, then conferring with Roger Pooley's edited version in the recent Folio edition, which has the advantage of being in large print so that I can consult it on a stand as I type in Bunyan's marginal comments and biblical references (in the left hand column).
In my notes, I'm giving the full text of each reference from the King James Version, unless the Geneva Bible translation looks like a closer source - Bunyan was familiar with both. If my comments threaten to grow into essays I will cut them short here, and expand on them in blog posts on the site.
I am grateful to all previous editors whom I consult along the way including the aforementioned Roger Pooley (Folio, and Penguin Classics), W. R. Owens (Oxford World's Classics) Neil Keeble (Oxford World's Classics) Roger Sharrock (Penguin, and Oxford English Texts (2nd Edition)), as well as Cheryl Ford's Devotional (Crossway) and her Faithfully Retold adapted text (Thomas Nelson), and George Offor's compiled notes of his own and predecessors (Banner of Truth, The Complete Works of John Bunyan).