Wow, thank you all for your generous responses. It will just be two of us so I think overlanding ourselves may not be cost worthy? Do you think? Also, what are the driving conditions like in Java? Is it as crazy as India or easier?
Great tip about Ramadhan, we will be sure to be in Bali by then. We would also like to trip over to Lombok and Gili Islands if possible too.
I will print up all of your suggestions and spend the evening planning my route!
Still it will be worth by an overland arrangement instead combining public land transportation with railways. Both of you just need a Toyota Avanza or Daihatsu Gran Max (including daily fuel+driver+driver+local guide+their board & lodging), which I believed still at your budget.
If refered to our tour itinerary which we had suggest, 85% of your journey will be in a good asphalt road & highway. The remaining 15% usually are under monthly maintenance from the government. No landslide or other severe damage on the asphalt surface. Regarding on driver behaviour in Indonesia, sure they aren't as neglect as those fellow in India.
Beside the state road capacity in here are still able to accommodate the traffic & our population in Indonesia or especially in Java island is less than India. So dont worry. We could share this info since we operate regular Intra Java Overland or Java - Bali Overland by our coachlines fleet.
Jakarta - Bali only require 28 hours traveling time (Includes lunch for one hour, dinner+take a bath for 2 hours, ferry harbor qeue+cruise for another one hour). Well, should anything else you need to know from us, please don't hesitate to inform us.