[en] We give the general prescription for calculating the moduli of irreducible, stable SU(n) holomorphic vector bundles with positive spectral covers over elliptically fibered Calabi-Yau threefolds. Explicit results are presented for Hirzebruch base surfaces B=F_r. The transition moduli that are produced by chirality changing small instanton phase transitions are defined and specifically enumerated. The origin of these moduli, as the deformations of the spectral cover restricted to the 'lift' of the horizontal curve of the M5-brane, is discussed. We present an alternative description of the transition moduli as the sections of rank n holomorphic vector bundles over the M5-brane curve and give explicit examples. Vector bundle moduli appear as gauge singlet scalar fields in the effective low-energy actions of heterotic superstrings and heterotic M-theory. (author)