We present new timing and spectral analyses of PSR J1412+7922 (Calvera) and PSR J1849-0001, which are only seen as pulsars in X-rays, based on observations conducted with the Neutron Star Interior Composition Explorer (NICER). We obtain updated and substantially improved pulse ephemerides compared to previous X-ray studies, as well as spectra that can be well-fit by simple blackbodies and/or a power law. Our refined timing measurements enable deeper searches for pulsations at other wavelengths and sensitive targeted searches by LIGO/Virgo for continuous gravitational waves from these neutron stars. Using the sensitivity of LIGOs first observing run, we estimate constraints that a gravitational wave search of these pulsars would obtain on the size of their mass deformation and r-mode fluid oscillation.