So many questions there. I'll try to perhaps give some suggestions. I think it's better to contact a tour agent separately in different cities that you plan to visit. Jakarta is a massive and developed city. It is a good starting location for touring West Java including Bandung, Mt Tangkuban Perahu, and Mt Krakatoa. I am not sure about a good travel agent there. Try to search these words in Google: Krakatoa or Krakatau tour, west java tour, ujung kulon tour.

Another location in Java that you referred to is perhaps Yogyakarta. This city is near to Borobudur Temple and Prambanan Temple. Alternatively you also can go to Surakarta (Solo). GA is flying from CGK to JOG and I believe to SOC too. Should be easy to find tours in both cities. Or you can rent a car and explore the cities yourself.

From there, you can then fly to Surabaya (SUB) direct or via Jakarta if you want to fly with GA. SUB is a big city so again should be easy to find a city or regional tour agent there. You can visit the mud volcano disaster area and perhaps visit some towns nearby like Malang and Batu.

From SUB you can then fly to Bali or if you prefer a not-so-crowded place then to Lombok. GA and Citilink are flying from SUB to Mataram (AMI) in the Lombok Island. If you feel more adventurous, you can fly to Labuan Bajo (LBJ) via Bali (DPS).