In answer to some of your questikns.
Book directly. No agent needed.
2/3 nights 2 days in sepilok jungle resort.
Pool.
Varied menu.
Day 1 - sepilok morning feeding, swimming, sepilok afternoon feeding.
Taxi from sandakan airport (prepay counter inside airport) £10.
Day 2 - rainforest discovery centre early or late, then sun bear sanctuary.
Trip to kinanbatangan river - tonnes of options but worth doing 3 day 2 night trip whichever you go for. All pick up in Sandakan.
We did Abai village homestay. Very basic, fabulous food (No choice), river trips, fishing, village visit. Massive highlight.
Booked directly.
Picked up from sandakan market (We had a night in sandakan before hand - stayed at sandakan backpackers which suited us well. There's a smart hotel with roof pool nearby).
Turtle island people are hard to get hold of. We didn't do this, but had info and provisional place through sandakan backpackers (emailed direct and they were far more responsive than crystal quest).
Then to kota kinabalu - 1 day white water rafting (look up riverbug trips) 1 day in marine national park snorkelling and doing island to island zip wire, Sunday market, eating freshly caught fish on water front.
That would probably fill your 12 days!
We also did 4 days on mantanani island for beach and snorkelling.
How did you get around. Taxi-super easy and cheap.
Was it safe enough - totally. Single parent + 3 kids 8-14. No problems.
Do check FCO for Turtle island as it was fco no go. Might invalidate travel insurance evrn if something unrelated happened there.
Budget - 16 days doing everything we wanted, but staying in cheaper (but safe and friendly) accommodation was £1700.