Backpacked there back in 04, so things have probably changed a bit since then…and as a solo bloke a different set of security parameters i suspect.
Sepilok for the Orangutan reserve – lovely place and a great experience
Mt Kinabalu – a strenuous trek to summit with an overnight at the lodge. A guide was obligatory but good value for the almost otherworldly location
Niah caves – the original Bat Cave. As the bats exit at dusk you are returning to the accommodation in the dark (not far) so a guide might be advisable, although the path was clearly marked. A proper jungle experience with the most impressive moths and bugs i’ve ever seen!
Kuching – a cracking little city with stunning old colonial architecture and temples
I had plenty of time to take it all in but Borneo (or more accurately Malaysian Sabah/Sarawak where i was primarily) is huge so flying around is a real option. Didn’t have or hear about any negative travellers experiences whilst there so would certainly recommend it.