48 hours gives you a lot more flexibility than 24 hours, obviously. In terms of food, I will still keep it predominantly Bosnian. Get burek with yoghurt for breakfast at least one day. Go to a traditional Bosnian spot for lunch one day (Srebrena školjka, Dzenita, or an ašćinica) and then get ćevapi the other day. Try two local spots for dinner: Nanina Kuhinja, Inat Kuća, Kibe Mahala one night, and then perhaps Avlija or Barhana the second night. For your afternoon coffee on one of the two days, take a taxi or tram to the Slastićarna Palma cafe and take a quick walk around the Grbavica neighbourhood to see some of the extant war damage.

In terms of which parts of the town to concentrate on, I would still keep it predominantly to the Austro-Hungarian and Ottoman parts. With your extra day, in addition to at least one of Galerija 11/07/95 and the War Childhood Museum, you could also go to the Sarajevo Tunnel. As with the 24 hour itinerary, definitely walk around Baščaršija and make sure to see the Sebilj, Gazi Husrev-beg mosque, the Latin Bridge, and the Vijećnica. Also make sure to walk along Ferhadija street and see the Eternal Flame. With two days, you probably can give an afternoon to Mt. Trebević - at the least, do consider taking the cable car up and checking out the old abandonned bob sled track (you don't need to go to the peak for this).

In the evening, as before, go to Zlatna Ribica for a drink, moving on to Birtija, or Sarajevska Pivara if you have the energy. If you happen to be there on a Monday, you have to go to Kino Bosna. On your second night you can try out Dekanter wine bar, The Bar, or Boardroom. Definitely try local wines (Žilavka or Blatina), beers (Sarajevsko, Gelender, or Brew pub), and rakija (any) in any of these places.