I'll try to answer your questions as best I can. Keep in mind that I rely primarily on Alexander Starbuck's History of Nantucket and Louis Coffin's Coffin Family. I have many other contacts and sources on the net, but of course they can all have errors.
As to question #1, the only Mary Bunker that would the wife of Tristram Coffin, son of John (son of Tristram) who founded the Martha Vinyard line of Coffins. Mary was born 1685 (according to Louis Coffin) and m. Tristram in 1714. As far as I can see, no other Mary Bunkers would fit into this time frame. Incidentally, Mary was the daughter of George Bunker, the founder of the Bunker line in Nantucket.
Hannah Brown, (question #2) is well documented. Through her, you will find that you are related to the Gardner family and the Hobart line. Thomas Gardner was co-founder of the Cape Ann colony in 1623 (You can read about him and his line in the book The Triumphant Captain John by Will Gardner) and the Hobart line can be traced back to the 1300's - the immigrants were a line of clergymen. Thomas Hobart was burned at the stake in 1555 in Essex, England for refusing to recant Protestantism. Hannah's parents were John Brown and Rachel Gardner. John Brown was the son of John Brown and Hannah Hobart (whom she was obviously named after. According to Louis Coffin, she married Jonathan in 1706. Hannah remarried after Jonathan's death which I am guessing was either in 1729 or 1730. She then married Tristram Coffin (Peter, Peter, Tristram). He died 13 Dec 1730, she in Feb 1731, no children. Perhaps they fell ill of the same disease) The children I have for Jonathan are: Jedidah, John, Deborah, Solomon, Zepheniah, Zerviah, and Hannah, the last born in 1728. All were the children of Jonathan and Hannah.
I doubt many of the children and dates in the St-Gelais gedcom. I have traced many of them to LDS data that is patently wrong, including the alleged marriage to Margaret Arthur who was married to Wilson Rawson, and whose daughter Pricilla was married to James Coffin (James, James, Tristram) In retrospect, I probably shouldn't have referred you to the St-Gelais site as there are many errors - witness the confusion at the beginning of the Pinkham line with the various Richards.
That should cover it - take it all with a grain of salt - everyone's data has mistakes in it. Thank you for your data - it will fill some blanks in my Pinkham lines.