Indonesia + Borneo + Brunei - creating an itinerary

Suggest you check out the itineraries at Friendly Planet. We met a father-daughter who used them for Borneo when we toured Turkey. Personally, I do check out where and what other tours do before setting out to design my own.

It’s been many years, but when we went to Indonesia we spent our full time on Java. It was a 3 week trip w a couple of nights in Singapore, so 2-1/2 weeks on Java. Indonesia is a big country so you will have to pick and choose — can’t see everything in 3 weeks.

I haven't been to Indonesia, so you can ignore this comment if you like, but I do know something about it -- it's a historically fascinating place that I had once considered visiting myself, though it didn't work out. Anyway, for what it's worth I'll offer the following comments:
[] The Indonesian part of Borneo, itself, is about the size of Spain, so two or three days there seem a little skimpy.
[] Brunei is tiny, but even so, in a single day you may not so much "see" it, as "glimpse" it.
[] The island of Java, mentioned in the preceding comment, and adjacent to Bali, holds the 1200-year-old Buddhist temple complex of Borobudur. There's a lot else on the island as well -- you may want to check the "Wikitravel" page on Java; it does a pretty good job of listing the island's tourist-worthy sites, and provides additional travel information as well.

I like the Bradt Guides for out of the way (at least for North Americans) places. They don't have an Indonesia guide but do have one for Borneo. That means their website should have something.
Depending on your age, travel method or interests, check out tours offered by Intrepid, GAdventures, Gate 1, whichever, that covers that part of the world to see what may catch your interest to replicate as a DIY trip.
I remember in a fit of boredom looking at Brunei, but there are some different rules and infrastructures for tourism, so check them.out before planning for more days or none at all.
Borneo needs at least 3 days even if all you do is Kuching and Sibu, let alone a liveaboard. (So say my kids)

I haven't been to Brunei, so can't comment.
Borneo is a big island, where Brunei, tiny country is. Part of the island belings to Indonesia and part of it belongs to Malaysia.

For your Indonesia portion, you can go to Bali, Yogyakarta (in central Java), Lombok island, Flores island.
In Yogyakarta you can do day trips to Borobudur temple and Prambanan temple.
You can find many liveaboard operators in Flores island. They mostly depart from the town called Labuan Bajo. They go to several small islands, including Komodo Island.
If you want to climb a mountain, you can go to Mt Bromo or Mt Ijen. Both are in East Java.

Make sure you hire a car with a driver. It's cheap over there and much safer than driving the car yourself.

In case you don't know. If you post in TripAdvisor, you will get so many responses from people, especially since your trip is not Europe focus.