All good information has been stated above.
The only thing I can add is that
Celebes Explorer is the only operator that guarantees Sipadan permits.
Are you are flying into Kota Kinabalu from Hong Kong? If so, catch an AirAsia evening flight from KK to Tawau (<$25 right now) and overnight in Tawau, or take a Malaysia Airlines early morning flight (<$35 right now). The dive operator you go with will pick you up in Tawau town or Tawau airport and transfer you to Semporna the morning that your package begins.
When your Sipadan dive adventure is finished, you can travel overland from Semporna to the Kinabatangan River. You can do this by private driver/taxi (expensive but might be worth it if you've got many bags with dive equipment) or public transport in minivans.
There are many resorts that do wildlife safaris on the river. You will see much more than just orangutans!
Not sure what needs you have for a sleeping set up, but there is something for everyone from bare bones to well appointed detached bungalows.
The two main areas for river safari operators are in Kampung Bilit and Sukau. Both villages are on the river. My advice is don't get sold a package that includes Gomantong Caves, Turtle Islands, and Sepilok. You do want a package that includes boat river tours, both day and night, because that is where you'll see the wildlife. The operator/lodge you choose can help arrange and figure out the transport from Semporna to their lodge.