On December 30th 2000, the Cassini-Huygens spacecraft reached the perijove milestone in its continuing journey to the Saturnian system. During an extended six-month encounter, the Composite Infrared Spectrometer (CIRS) returned spectra of the Jovian atmosphere, rings and satellites from 10 to 1400 cm^-1 (1000 to 7 µm) at a programmable spectral resolution of 0.5 to 15 cm^-1. The improved spectral resolution of CIRS over previous infrared instrument-missions to Jupiter, the extended spectral range and higher signal-to-noise performance provide significant advantages over previous data-sets. Both optimal-estimation retrieval and radiance-differencing are used to investigate the global variation of upper-tropospheric temperature, ammonia, phosphine and cloud opacity between ± 60˚ latitude. The analysis methods are shown to successfully reproduce Jovian conditions with results consistent with previous investigations. The composition results in particular are well characterised and suggest an important role played by mixing and transport within the upper-troposphere. Interpretation and validation of the retrieved results is conducted via the construction of a simple dynamic model incorporating transport, diffusion and (photo)chemistry.