In this paper, we describe the XENON100 data analyses used to assess the target-intrinsic background sources radon (222Rn), thoron (220Rn) and krypton (85Kr). We detail the event selections of high-energy alpha particles and decay-specific delayed coincidences. We derive distributions of the individual radionuclides inside the detector and quantify their abundances during the main three science runs of the expe...