For the recoil mass, you have to use the mass of the Hydrogen atom including the nucleus - not just the electron. With that the recoil energy becomes very very small, as a proton is about 2000 times heavier than a naked electron.
A similar effect occurs in the Moessbauer effect. When a Moessbauer nucleus in a crystal lattice emits a gamma ray, the recoil energy is taken up by the entire crystal lattice, not just by the emitting nucleus. This allows relative bandwidths of Moessbauer lines in the delta E/E = 10^-15 range.
Stokes shifts are observed when excitations exist that have zero or negligible net momentum transfer, e.g. vibrational and rotational modes of molecules or crystals. Apparently the rotational modes of hydrogen molecules H2 are quite easy to observe.
If you had a hydrogen crystal then it might be possible to observe Stokes and Anti-stokes shifts corresponding to optical phonons at momentum transfer=zero.