What to do in Jakarta
It depends on how long you want to stay at Jakarta. If you want to stay a day there make sure you arrive at Jakarta in the morning so you can go for sight trip before you head to Bandung. There are a lot of sight places to go. You can get the details on Lonely Planet. I bet a day is not enough. If I were you I’ll avoid fancy shopping complex as I can easily go at my own place.
Jakarta – Bandung
To Bandung, you can go there by train. http://www.kereta-api.co.id/index.php This is the site where you can buy the ticket online. You can take the train from Gambir. If Gambir is inconvenient, you can also get your ticket at the Senen Station, or the Gondangria Stations, both of which may be closer to your hotel.The best train service for Jakarata is theParahyangan (business/executive 45, 000/60, 000Rp, three hours), with departures roughly every hour from 4am to 8.25pm.
What to do in Bandung:
Stay in Braga City Walk which is commendable especially for the fact that it is quite near to every place you will plan to go (like I know!?). Jalan Dago area, Tangkuban Perahu and Natural Strawberry Farm then Kg daun and later to Rumah Mode/Mode Plus + Toko Tiga. Pasar Baru (half day was apparently enough). Afternoon at Jalan Riau (2-3 FOs were enough to call it a day). Kartika Sari and Sari Pawon. Not to forget Dago Thee Huis for art performance. Most of the places I suggested are for shopping and eat, you can go to Lonely Planet to find sight place but not much at Bandung.
Bandung – Yogyakarta
Several trains operate on the Bandung–Banjar–Yogyakarta route, most continuing on to Surabaya. Most are night expresses, such as the business-class Mutiara Selatan, which passes through Bandung at 5.05pm on its way to Yogyakarta (80, 000Rp) and Surabaya (120, 000Rp). The Lodaya leaves Bandung at 8am for Yogyakarta and Solo (business/executive 90, 000/150, 000Rp). For buses, Kramatdjati (4239860; Jl Kebonjati 96) and Pahala Kencana (4232911; Jl Kebonjati 90) run luxury buses to long-distance destinations, such as Yogyakarta (81, 000Rp). Usually takes 5 hours.
What to do in Yogyakarta
Benteng Vredeburg Museum
The architecture is worth a look, but the dioramas are designed for Indonesian patriots.
The fine old wooden houses here contain an outstanding collection of kris, a few wayang puppets, batik and basketry and some historic photographs of Yogya. There’s a highly recommended restaurant and accommodation too. To get to Tembi, jump aboard any bus bound for Parangtritis beach from Jl Parangtritis and get off at kilometre 8.4 on the highway; Tembi is 400m east of here along a side road.
Paintings, including some astonishing self-portraits
A splendid pleasure park of palaces, pools and waterways for the sultan and his entourage. The Portuguese architect of this elaborate retreat, built between 1758 and 1765.
Borobudur it takes about 45 minutes to 1 hour by bus.
Merapi Volcano! Water Temple! Pantai Sundak!
And a lot of shopping places I don’t have to write here. You can easily search on internet.
Yogyakarta - Surabaya
Lots of choices to choose from, especially for the night express bus. If you go to the bus station, there will be lot more choices. One of reliable one is Safari Dharma Raya. It's executive bus departs Yogya Giwangan terminal at 7pm and arrives at Surabaya Bungur Asih Terminal at 4am (all intercity buses from Yogya arrive at Bungur Asih in Surabaya) Other serving the route: AKAS, Mira, Eka, etc... All has moreover similar departure time. Alternatively, for more comfortable journey (but little expensive), take train. Mutiara Selatan, Bima, and Turangga (all executive class trains) depart past midnight from Yogyakarta and you'll arrive in the morning. Train departs from Tugu Station in Yogyakarta and arrives at Gubeng Station in Surabaya. Executive class seat in Indonesian train is equivalent to First Class seat in European.
What to do in Surabaya
Even though much of Surabaya's historical centre is literally falling to pieces, the old city easily wins the 'Most Attractive Neighbourhood' prize. With crumbling Dutch architecture, strong Chinese influences and an Arab quarter, it's also the most interesting and idiosyncratic. A good place to start exploring the old city is Jembatan Merah, the so-called 'Red Bridge' that saw fierce fighting during Indonesia's battle for independence.
House of Sampoerna
Just northwest of Jembatan Merah is the city’s best-presented attraction, the House of Sampoerna which is the home of one of Indonesia’s most famous kretek cigarette manufacturers. Whatever you think about the tobacco industry, this factory and museum makes a fascinating place to visit. The building itself is a wonderful 19th-century Dutch structure, originally an orphanage but later converted into a theatre (indeed Charlie Chaplin once dropped by).
Monumen Kapal Selam
In keeping with Indonesia's fascination with all things military, Surabaya's foremost stretch of renovated, waterside real estate centres around the hulk of the Pasopati, a Russian submarine commissioned into the Indonesian navy in 1962. The Pasopati itself is well maintained and there is a small landscaped park with a couple of cafés popular with young smoochers.
To the east of Jembatan Merah is Surabaya's Chinatown, with hundreds of small businesses and warehouses. Becak and hand-pulled carts are still the best way to transport goods in the crowded, narrow streets.
From Suribaya's old city you can then head north to the Kalimas harbour, where brightly painted pinisi from Sulawesi and Kalimantan unload their wares.
And visit Mount Bromo and Ijen Crater, more cool restaurant and entertainment places to visit.
Surabaya – Bali
If you prefer to take train, there is only 1 business or executive train serving Surabaya - Banyuwangi route which is Mutiara Timur. Train will terminate at Banyuwangi Baru station which is just few hundred meters from Ketapang ferry terminal. After reach Gilimanuk, continue your journey to Denpasar by bus. The train company sell combo ticket (train + ferry + bus) ride between Surabaya to Denpasar.
Please do so. It's just the same like having a trip from KL to Langkawi but you want to stop at Cameron Highlands. The main difference here is there is NO north-south expressway as Peninsular Malaysia has, so hitting the road will take much time in here, besides Bali is much larger than Penang island. Hence, to make the most of your trip to visit as many places as possible, flying is the best thing to put into consideration.
What to do in Bali
You got everything in Bali, but just a reminder, Bali is a bit pricey as it is main attraction in Java island. So you really have to spend less money on hotel and food. Go travel Bali, try all activities there such as go swim with dolphin, bungee jump and more. Read more here, because there are A LOT of things and it would never end if I write it here.
Total for expenses (excluded activities fee/entrance/shopping and food) is about RM 650. From my estimation RM 2500 is enough including flight ticket from KL - Jakarta and Bali - KL. It will be much cheaper if you know how to cut the expenses on food and accommodation.