Analysis of T dwarfs using model atmospheres has been hampered by the absence of reliable line lists for methane and ammonia. Newly computed high temperature line lists for both of these important molecules are now available, so it is timely to investigate the appearance of the various absorption features in T dwarfs in order to better understand their atmospheres and validate the new line lists. We present high quality R~5000 Gemini/NIFS 1.0-2.4 microns spectra of the T8 standard 2MASS 0415-0935 and the T9 standard UGPS 0722-0540. We use these spectra to identify numerous methane and ammonia features not previously seen and we discuss the implications for our understanding of T dwarf atmospheres. Among our results, we find that ammonia is the dominant opacity source between ~1.233-1.266 microns in UGPS 0722-0540, and we tentatively identify several absorption features in this wavelength range in the T9's spectrum which may be due entirely to ammonia opacity. Our results also suggest that water rather than methane is the dominant opacity source in the red half of the J-band of the T8 dwarf. Water appears to be the main absorber in this wavelength region in the T9 dwarf until ~1.31 microns, when methane starts to dominate. ; Comment: 29 pages, 37 figures, accepted for publication in MNRAS