Hi, DCA-SEA. I'm an American Expat living in JKT, and that said, JKT is probably one of my least favorite cities; however, Indonesia is one of my favorite countries. If you do decide to spend a bit of time in JKT, two to three days is more than plenty. Not a lot of museums, but plenty of shopping and spas if that is your type of thing. Some nice parts of the city to explore, but can VERY difficult to move around, the city has horrible infrastructure, traffic is a nightmare. Surabaya isn't much better. Jogja, is amazing, and I think Malang and the areas around it are interesting to explore as well. What I might suggest:

Arrive CGK. Spend a couple of days, get over JETLAG. Flight to Jogja or Danu Toba for a few days. From either one of those places, head to Lombok. Spend time there, and onto Gili Islands for some time as well. Or, Komodo can be a must see too. Feel free to PM me with specific questions. Good luck planning!