We present a rigorous derivation of the nuclear spin-rotation and spin-torsion coupling terms in the hyperfine Hamiltonian for molecules with internal rotation. Our formulas differ from the expressions derived by Heuvel and Dymanus [J. Mol. Spectrosc. 47, 363 (1973)], which these authors used and which were also applied recently by others to interpret experimental hyperfine spectra of such molecules. In the present work, our theoretical results are applied to methanol. We calculate the nuclear spin-spin magnetic dipole-dipole interactions and the nuclear contribution to the spin-torsion coupling vectors from the nuclear coordinates as functions of the internal rotation angle γ, compute the spin-rotation coupling tensors by ab initio electronic structure methods also as functions of γ, and obtain the missing parameters for the electronic contribution to the spin-torsion coupling from a fit to measured spectra. The resulting hyperfine Hamiltonian is then used to compute hyperfine transition frequencies and intensities for twelve torsion-rotation transitions in methanol. With the use of the ab initio calculated spin-rotation coupling parameters without any modification, and physically reasonable values for the spin-torsion coupling parameters from the fit, we find good agreement with all of the measured spectra.