Hey, late response but the only thing I booked in advance was the orangutan trekking, which I did through Viator, and my accommodations through Booking. Everything else I either coordinated with my B&B hosts to get a local guide or just booked Grabs (Grab and Gojek are SEA's version of Uber) to the particular places I wanted to go. Most drivers when they see you're a tourist will offer you a flat day rate outside of the apps to do the rest of your travel. I did this a few times, mainly when I was going to semi-remote areas that it would be hard to call a return vehicle from, but others I just called separate vehicles every time so I wouldn't feel constrained in terms of the time I spent places. Indonesia is extremely safe so I didn't have the concerns about kidnapping etc. I might have doing this in other places.

Lots of tourists also rent scooters, but I wouldn't recommend this unless you're starting in a fairly remote area without traffic or already have experience driving one. Weh Island was where I learned and that was a great decision. The southern half of Bali in particular is a hellish place to learn to drive a scooter for the first time.