We study normal transport and the subgap spectrum of superconductor-normal-superconductor (SNS) junctions made of semiconducting nanowires with strong Rashba spin-orbit coupling. We focus, in particular, on the role of confinement effects in long ballistic junctions. In the normal regime, scattering at the two contacts gives rise to two distinct features in conductance: Fabry-Perot resonances and Fano dips. The latter arise in the presence of a strong Zeeman field B that removes a spin sector in the leads (helical leads), but not in the central region. Conversely, a helical central region between nonhelical leads exhibits helical gaps of half-quantum conductance, with superimposed helical Fabry-Perot oscillations. These normal features translate into distinct subgap states when the leads become superconducting. In particular, Fabry-Perot resonances within the helical gap become parity-protected zero-energy states (parity crossings), well below the critical field Bc at which the superconducting leads become topological. As a function of Zeeman field or Fermi energy, these zero modes oscillate around zero energy, forming characteristic loops, which evolve continuously into Majorana bound states as B exceeds Bc. The relation with the physics of parity crossings of Yu-Shiba-Rusinov bound states is discussed.