When do you plan to travel? I recommend that you fly as advance resv on budget airlines will be affordable and less exhausting. Presently, the east Malaysian states are encountering mid- year raining season not conducive for long interstate/inter country rides (across Brunei).
Yes it is and vice versa. There are a few bus companies available but the recommended one by Intrepid journey and Peregrine can be found on trip advisor. I wouldn't bus or train in the rainy season tho. You do get to see a lot overland and I prefer it but plane is quicker and probably safer in bad weather!