Well since your flight home won't leave till evening you can use Amanusa facilities all day or I suggust booking two nights. The beach at Amanusa is a lot nicer then Amankila's and your 15 min. to airport. The food is really good and you'll like the rooms. It's really underrated and over looked.
Do Amanwanna first, then over to Amanjiwo, and then two nights at Amanusa. The beach at Amanwana is just to look at as its all crushed coral and you can't walk barefoot on it. If you can find time to do Komodo on their boat make sure you do it. We were the only guest on it and spoiled rotten. The seaplane transfer is a nice way to eliminate the long return and you get to see some amazing site's.
I understand we all have to get back to work but your gonna feel rushed with only 4 days at Amanjiwo. There's so much to see and you gonna want to just stay at the resort for a few days.
June is really nice just go toward the end as the weather will at its peak with clear blue skys in Java.