You may not need a standard tour for this sort of on-the-beaten-track itinerary. I just returned from a couple of weeks in Indonesia on my own, with a loose itinerary, a few advance hotel reservations done by internet, and a bunch of making-arrangements-on-the-fly. My itinerary was:
Fly KUL-Jogyakarta. 4 nights in area, including 1 at Borobudur. Taxi from airport to town. Then used becak in Jogya and public bus (cheap and easy) from Jogya to Borob and back, also to Prambanan and back.
Train Jogya-Surabaya, ticket bought myself at the Jogya station a day in advance. Original plan to go by minibus to Mt. Bromo area of East Java had to be scrapped due to advice about rainy weather obscuring the views and making the trip worthless. (This wouldn't be a problem in summer though.) 2 nights Surabaya, local taxi for sightseeing. Tip: hit the House of Sampoerna museum and their free 1-2 hour tour bus around old Surabaya landmarks.
Flgiht Surabaya-Makassar on Sulawesi, had hotel in SUB get it for me a day in advance. 1 night Makassar (dump of a city), purchased outbound Makassar-Jakarta domestic ticket, and then luxury daybus to Tana Toraja area (reserved seat day before).
3 nights Rantepao (Tana Toraja), hotels found on the spot due to low season, but make advance arrangements for high season. Local becaks for short jaunts, also engaged a local guide with car and driver there for 2 days' services around the TT area. Luxury night bus directly back to Makassar airport (ticket purchased 2 days before) then morning flight to Jakarta. 2 nights Jakarta, then flight back to KUL (intl flights prearranged well in advance).

You could do similar, suggest you try routing itinerary to fly internationally into Bali directly. Then go overland (make arrangements once in Bali) via road and the short ferry hop to Java, do East Java/Mount Bromo. This is a very common trip taken by loads of travellers. Then overland (make arrangements there, it's also a common routing) to Jogya. Or if you despise long (11 hour) road trips, get from Mt. Bromo to Surabaya and then train or fly to Jogya and Borobudur. Then fly via Jakarta to Medan in Sumatra and make arrangements to get to Lake Toba from there. Or stay in Jakarta a day and make arrangements there to be met in Medan and taken to Lake Toba by a driver. Depending on where you are headed next, you can exit Indonesia from Medan (to PEN, KUL, SIN and onward) or back to elsewhere via Jakarta. Or in reverse--starting in Medan/Lake Toba and routing via Jakarta to rest of Java, then to Bali, exit intl via Bali.

You'll likely find getting from East Java or Yogya to Sumatra will require at least a transit in Jakarta airport. Suggest minimizing time in Jakarta unless you have business there--not much to see for the casual traveller. Really, this is an easy trip to self-set up. Just make some hotel arrangements in advance and deal with the domestic travel items once there. Try to minimize backtracking and minimize # of times going through Jakarta. International flights in/out best arranged in advance, and I found "open jaws" into Jogya and out Jakarta no more expensive than a straight round-trip, and loads more convenient. To me, it seemed much easier getting around with a good guidebook and a tiny bit of advance reading for historical/cultural stuff. And engaging a local guide at appropriate places (i.e. Tana Toraja). In Indonesia, ALWAYS use a local guide for local areas, never a non-local Indonesian.

My largest expense was for hotel (I am a mid-range type of person), but this is a matter of style and preference. Everything else, including Indonesian inter-city and local transport (and guide when needed), was much cheaper. I estimate my total cost was about 1/2 of what the same items would have cost, done as a packaged or pre-arranged tour. And I found very little time was "wasted" in whatever logistic/onward transportation items I needed to find and purchase as I went along.