2 months in Indonesia

Well, that list only has 6.5 weeks' of places to visit, which would probably leave enough time (out of 2 months) to travel between them.
If going to Banda and Raja Ampat, I'd drop the Gilis unless they are there for partying.
Other than Banda, all places on the list are readily accessible so this plan might be doable. Banda should be carefully planned around Pelni schedules.

Hi

Maybe you can start from Flores.

1) Flores-Lombok-Gili-Bali.
Take a flight from Bali/Jakarta to Flores, spend your time go to Lombok,Gili than Bali

2) Banda
You need to go to Ambon if you wanna go to Banda. There is also a regular flight from Denpasar (Bali) to Ambon via Makasar. You have 2 option: by PELNI boat (check on their website for schedule) or another ferry from Tulehu, about 1 hour from Ambon, leaving each satuday from Ambon to Banda and Banda to Ambon each thusday.

3) Raja Ampat
From Ambon, take a flight to Sorong or by PELNI boat. Sorong-Waisai by ferry and usually depend on where you will stay, they will pick you up in Waisai (capital of Raja Ampat).

4) Toraja
From Sorong,take a flight to Makasar, and Makasar to Rantepao(Toraja) by bus or airplane.

Hope this will help :)

Wow, thanks for information! Apart from these places is there anything you would not recommend to visit? As Laszlo said for example Gili islands should be visited unless for partying.

The Gilis are part of Lombok and very short boat ride between all the West Gilis. Southern Lombok more picturesque and their Gilis are said to be better for snorkeling, although I am not a fan of this area in general..
Also, if you do indeed have more time then Sumba is a fascinating place.

All your other places are worth visiting, though I would also happily swap Lombok for Sumba any time.
If transport to Banda turns out too difficult, spend that week on Ambon, Saparua and Nusalaut instead. They offer similar attractions, minus the volcano, but ade far more accessible.

This is such a complicated country to plan a trip... So I guess I'll swap Lombok to Sumba and won't go to Gili Islands (still I'm not a big party person). I had chosen Banda islands for my last week in Indonesia where I could just relax, enjoy white-sand beaches with crystal clear water and amazing views while also avoiding tourists. As Laszlo mentioned, would Ambon, Saparua and Nusalaut would be something similar to what I'm looking for or there is a better place which comes to your mind?

The reason the Bandas have few tourists is because it's difficult to get to. If it was easy to get to, it would be teeming with tourists.

Nusalaut is an island that sees about 3 tourists a year. That corner of Indonesia is lovely for a little bit of history, nice village life, beautiful landscapes, and great water for swimming and snorkeling. It's not really a place for beautiful beaches (nor are the Bandas). You might want to look into the Kei Islands for beaches...

And sure, Indonesia's enormous, with a ton of choices, and you only have 2 months. You're inevitably going to miss out on lots of lovely places. Don't worry. You can go back.

I actually think Saparua's beaches a pretty good, while Nusalaut offers better snorkelling. Last time a friend went to Nusalaut, the guesthouse in Ameth actually had 3 couples from 3 European countries staying there at the same time, though I personally never bumped into other tourists on the island.
The Keis obviously have superior beaches, but lack the other sights of the Ambon-Lease group.
Mind you, Raja Ampat is hard to beat. It might be better to leave that for the end.

So I guess I'll swap Lombok to Sumba

By the way, there is the Pasola festival happening every year in February and March on Sumba, which perfectly links up with your travel period! Just note that the exact date hasn't been announced yet, so you will need to be flexible if you want to be there at the right time.

If you want to see nature, somekind of mountain, waterfall and virgin beach you can go to malang city in java island. You can go to bromo mountain, semeru mountain or waterfalls and many other beautiful place. You can browse about the picts of bromo mt, tiga warna beach, bidadari waterfall, etc all that place is in Malang. If you curious about beautiful hiden place in java you can ask me. I'll show you.