Recent advances in quantum technologies have enabled the precise control of single trapped molecules on the quantum level. Exploring the scope of these new technologies, we studied theoretically the implementation of qubits and clock transitions in the spin, rotational, and vibrational degrees of freedom of molecular nitrogen ions including the effects of magnetic fields. The relevant spectroscopic transitions span six orders of magnitude in frequency, illustrating the versatility of the molecular spectrum for encoding quantum information. We identified two types of magnetically insensitive qubits with very low ("stretched"-state qubits) or even zero ("magic" magnetic-field qubits) linear Zeeman shifts. The corresponding spectroscopic transitions are predicted to shift by as little as a few mHz for an amplitude of magnetic-field fluctuations on the order of a few mG, translating into Zeeman-limited coherence times of tens of minutes encoded in the rotations and vibrations of the molecule. We also found that the Q(0) line of the fundamental vibrational transition is magnetic-dipole allowed by interaction with the first excited electronic state of the molecule. The Q(0) transitions, which benefit from small systematic shifts for clock operation and is thus well suited for testing a possible variation in the proton-to-electron mass ratio, were so far not considered in single-photon spectra. Finally, we explored possibilities to coherently control the nuclear-spin configuration of N2+ through the magnetically enhanced mixing of nuclear-spin states.