It's been a long time since our cruise through Indonesia, but the logs below can give you some ideas about places to stop. Must see: Rinca (Rinja) island, where there are also Komodo dragons. Hint: they're pretty nasty, so don't go ashore alone, but do keep your camera with you at all times, my best pictures were from the cockpit in the early morning when everything came down to the water. This is an amazing and quiet island, no people, no tourists to distract from the wildlife. (Darwin to Sumbawa log).
The island across from Bali, Lombok, is pretty wonderful.
Darwin to Sumbawa
Lombok and Bali
Practicalities. April is still cyclone season.
Be sure you have good tide tables. WXtide is downloadable and gives you tide tables world-wide. You will need them!
In my opinion, the PNG islands east of mainland PNG are more interesting than mainland PNG, unless you want to stay in Port Moresby and travel inland. Easier, IMO, is to sail over to Gove, then on to Darwin, and up to Indonesia and really see Indonesia. You know that you have to obtain a cruising permit to go through Indonesia, right? Don't know what it's like now, used to be a real PITA and rather pricey to get it. Do your homework there, it's not an easy thing to accomplish.
My enduring images of Indonesia are of the beauty that they bring to everything - their boats are beautifully painted and decorated (even the everyday fishing boats) - the little Bali boats that individuals go out fishing in every night - all their decorative arts. My biggest annoyance with Indonesia - buying anything is not easy. You have to haggle over the price of everything. Everything. On the other hand, once you get used to it, it's just a game that you have to play to earn the locals' respect.
Another way to go is the Darwin-Ambon yacht rally which starts from Darwin in August, 2013. Organized by the Dinah Beach Cruising Yacht Association, it's a lovely way to meet fellow cruisers and have a good time. My only comment is that it's 'way far north of your route to Bali and you might miss a lot going that way. Get a really big map of that part of the world to help you decide what route to take.
I'd go back through Indonesia in a heartbeat. Loved it. All of it.