So after more research this past weekend I'm thinking to limit the Java portion to the area Yogya-Solo-Magelang. I really don't want to be viewing Indonesia from a car window. I want to be out and about walking, seeing temples, hiking some, visiting museums, and of course some shopping. I prefer to stay in each location at least 2 nights before packing up and moving on changing hotels.

Here is a sample itinerary that looks like it would work with some tweaking and additions:

Day 1 Arrive SOLO – YOGYAKARTA (L,D)
Meeting service at Airport in Adisumarmo-Solo, then visit Prambanan Temple it's the biggest temple complex in Java. With 224 temples in the complex; three of them, the main temples are Brahma Temple in the north, Vishnu Temple in the south, and the biggest among the three which lies between Brahma and Vishnu temples is Shiva Temple (47 meters high). These three ancient masterpieces of Hindu architecture are locally referred to Prambanan Temple or Lorojonggrang Temple. Afterwards, proceed to Yogyakarta for check in. Evening program, seeing The Ramayana Ballet
Day 2 YOGYAKARTA CITY TOUR (B,L,D)
After Breakfast at Hotel then visit : Sultan Place officially named the " Kraton Ngayogyakarta Hadiningrat ", a grand and elegant example of Javanese architecture, "Tamansari" Water castle, Museum Chariot and Kota Gede. After Lunch at local Restaurant; continue to Kasongan, Bringharjo and Malioboro sight seeing as the ultimate program, and then drive to Borobudur for stay in Manohara Hotel, the closest hotel to Borobudur temple.
Day 3 BOROBUDUR SUNRISE (B,L,D)
Enjoy the wonderfull Sunrise in Borobudur Temple early in the morning. After Breakfast at Hotel, depart to Solo. On the way, stop at Mendut Temple and Kaliurang to see the scenery of mount Merapi and if you are lucky you will see the Lava fall down from the top. Drive to Solo and stop at local restaurant for having lunch. Arrive and stay overnight in hotel.
Day 4 SOLO TOUR (B,L,D)
After Breakfast at Hotel, then visit: Mangkunegaran Palace – Solo, Cetho Temple the erotic temple and Sukuh Temple. Lunch will be provided in local Restaurant. Back to the hotel at noon. Evening, transfer to local restaurant for having dinner.
Day 5 Transfer Out (B) to ?

Any ideas of sites or places to visit in these areas?