This is a re-worked itinerary for a 30+ days trip. We sacrificed the eastern part of Indonesia for Borneo, and I think this works better for us. Nothing is set in stone yet, just the flights, so please take a look at this and let me know what you think. We are a couple in our late 50s, early 60s, interested in wildlife, nature, architecture, good food, beautiful views, culture, temples.

Land in Kuala Lumpur, spend 3 full days there, with a day trip to Kuala Selangor to see Silvered Leaf Langurs
Day 4 - Flight to Sandakan Airport. We'll join a Borneo tour there for 5 nights. They are bringing us to Kota Kinabalu on day 10, and we'll spend the night there.
Day 11 - flight to Denpasar via Kuala Lumpur. This is going to be long, but I don't see any other option with our itinerary. We'll have 7 full days in Bali, probably 2 destinations. One Ubud and another one.
Day 19 - Travel to Surabaya (non-stop flight) for Bromo. Stay there 3 nights, 2 full days. One day for the volcano, and one day for some birding.
Day 22 - Travel to Yogyakarta via Denpesar; transfer to Borobudur. 3 nights, 2 days there. One for the temple, one for the Dieng Plateau.
Day 25 - Transfer to Yogyakarta; 3 nights, 2 days there for the temples and the Ramayana ballet performance
Day 28 - Flight to Singapore, 4 full days there, with one set aside for birding.

What do you think? Is there a better way, logistically to organize this? Any place you would suggest a longer or a shorter stay? Thank you.

I can't help but I will be following along. We want to visit SE Asia including Singapore and Malaysia. So your itinerary interests me. We are only collecting ideas right now. Nothing concrete. When is your trip? What is the name of your Borneo tour operator? My husband has mentioned Borneo but I think I would only feel comfortable going with a tour group. Thanks!

We'll be there July-August, and working with Borneo Eco Tours for this tour: https://www.sukau.com/all-tours/borneo-big-5/
Nothing is booked yet, I'll let you know how it goes.

Why go from Surabaya to Yogyakart via Denpasar? There is a train.

Honestly, because I didn't even consider trains. Great point, thank you!!

@ KarenWoo: Have you seen my trip report? You might find it of use.

kja, I see you have two. One for Cambodia and one that includes Singapore. I will save them to my desktop. Thanks!

Grew up in Malaysia and I would say if you are interested in history and culture at all you might want to try the UNESCO-listed colonial port towns of Georgetown and Malacca. Lots of beautiful heritage buildings and cultural sights to visit around there like the Pinang Peranakan Mansion and the Dutch Square. Penang is also renowned for having some of the best food in Malaysia, for what it’s worth.

Is it safe to go to Sandakan right now? It's appearing on the foreign office list of advise against all but essential travel - it's where we'd like to go but worried about safety and insurance!

can anyone advise please?

Menjangan Island in Bali is sooooo beautiful! It is really worth it!