The 5-7 days in Bali and 2-3 in Yogja sounds about right. Flights are all direct and plentiful.

Any travel away from the usual tourist spots takes time. 100km drives take 8 hours. Stuff stops working for no reason. Flights are canceled. If you head over to KK, 2-4 nights is probably not enough, you'll waste most of your time in transit. If you decide to give it a go (hey it's some adventure!) be sure to do it first in case something happens.

Make sure to push your trip at least a week after Ramadan. Everyone in Indo goes home and they'll be coming back to work after that so transport can be congested. Ramadan isn't a bad time to travel either, Bali is empty of most local tourists (although August is high season for the Aussies), and you'll get a different slice of life in Java and KK.

Your total trip is 14 days, that's about the minimum you'd want to spend after the 36 hrs it'll take you to get here from the US.

Peace!