Museums: Jumping on the Jacquemart Andre bandwagon -- I've had a lovely experience doing it at night on the late closure evening. Also the Musee de la Chasse et de la Nature (that may be a personal preference... if you enjoyed Deyrolle, go -- if taxidermy makes you squeamish, avoid.) Also, since you've seen the highlights at other museums, I like Bets' suggestion to hit up exhibits that interest you. Lovely to swoop in, see what you're into, and swoop out without feeling pressured to manage the crowds.
Off the beaten path, in the city: Check out the 10th/11th/20th -- my favorite part of the city. Lots of very reasonable and interesting restaurants, and few tourists are willing to venture that far. Since you are a coffee fiend, check out Cafe Oberkampf, tucked away off Rue Oberkampf. (Fair warning, it's tiny and VERY popular, but for good reason.) Also, it's not exactly off the beaten track, but I love the little coffee shop that is part of the Merci store on Blvd Beaumarchais (3eme) as a nice place to stop for a rest.
Food market, city: Marche Aligre, just east of Bastille -- both the street market (along Rue d'Aligre), as well as the covered market. Plus, that puts you near Baron Rouge for a little oyster snack.