Flights from Kalimantan to Indonesia

Hi!

For the moment I am in Sabah (Maleysia) but in the end of this week I will hopefully be in Indonesian Tarakan to travel through Kalimantan.
Since I am travelling throughout South East Asia I want to go afterwards from Kalimantan to Nusa Tengara (Flores, Lombok, Sumbawa)
My question now is: what is the best budget option to travel from Kalimantan to Flores?
I need to start at Flores and then go directon Lombok etc.
I thought that I could fly perhaps from Balikpapan to Sulawesie and then hop to Maumere Flores but this doesn`t seem possible?
I have been searching the internet to find flights but they all seem to suggest flying to Kuala Lumpur, then to Jakarta, then to... and then, finally fly to Maumere. Even if the flights are cheap, it still will cost a lot of money!
Is there anyway how I can figure out, on the internet, how I need to plan my destinations or book my flights?
I find it rather complicated to figure out on which destinations all these smaller airlines fly...
Has anybody experience in taking a Pelni-ship from Kalimantan to Flores? (Duration? Cost?)

A big thank you!