Combining Jakarta-Borobudur and Kuala Lumpur-Georgetown (Penang) in a week is possible, of course. But I don’t really see why you would want to do it. There are multiple factors at work here. The first is flights and fares: you don’t tell me where you’ll be travelling from, but assuming Delhi as the point of departure, you’ll find that many flights to Jakarta are routed via KL (there are no direct Delhi-Jakarta flights). On the face of it, this would strengthen the argument for adding Malaysia to your trip. Georgetown is then only an hour’s cheap flight away from KL. However, bear in mind that a) airlines usually charge extra when you want a stopover rather than transit, and b) you’ll need a visa for Malaysia (another ?4k-odd per person). You’ll have to return to KL to take another flight to Yogyakarta (bypassing Jakarta altogether), which is another two-and-a-half hours. All this is complicated, and will probably make your trip more expensive.
But costs and logistics apart, if I were you, I’d stick to a purely Indonesian trip. I’d prefer to immerse myself in one country and its culture rather than mixing places and experiences. For people interested in heritage and culture, a week in Indonesia sounds like a good, focussed as well as relaxed plan. This way, you can give yourself a couple of days in Jakarta, taking in its considerable built heritage. Attractions here include the colonial neighbourhood of Old Batavia, the heart of which is the Taman Fatahillah Square. On the west bank of the Kali Besar canal, 18th-century homes still stand. Spend at least one evening seeing a traditional Javanese dance drama, known as wayang wong, at the Bharata Theatre—the language may be unfamiliar but the myths and stories will reverberate with all Indians. Contemporary performing arts are showcased at the Taman Ismail Marzuki Arts Center. Hotels in Jakarta tend to be affordable, and if you’re not looking for luxury, try one of the three Ibis Hotels in the city (from ?2,600; www.ibis.com).
Once done in Jakarta, take the one-hour flight to Yogyakarta, the base for your visits to Borobudur, Prambanan and other heritage explorations. Check into a hotel in Yogyakarta and figure out which of the other numerous heritage sites you want to visit. Borobudur is an hour’s drive from Yogyakarta (get there at sunrise and avoid weekends). The fabulous Prambanan temple, another Unesco World Heritage Site, is just outside Yogyakarta and can be done on another day. A third day can be given over to the rest. You might find http://architectureofbuddhism.com/books/borobudur-yogyakartanearby-7-day-itinerary/ useful when planning your Yogyakarta days. Do also download the fact sheets on Borobudur, Prambanan and Ratu Boko, available at the official site, http://borobudurpark.com/fact-sheet/. These have details of timings, entry fees, etc. There’s a plethora of good hotels in Yogyakarta, and you can choose between resorts, boutique hotels, colonial-style ones—most of them available for under ?3,000 (even the well-rated Hyatt Regency has rooms from about ?3,600).
As far as transport goes, the most comfortable options are: flights between cities (although train/bus is possible) and hired taxis for the day when doing a circuit of heritage sites (though buses are an option). September is a good choice. This will be the end of the dry season, which lasts April to October, and will also coincide with the end of the tourist season (so, possible to get decent deals on hotels and tours).