High-resolution, high-throughput soft X-ray spectroscopy using reflection gratings has the potential to unlock answers to many of the questions about the high-energy Universe. To enable missions to use this technology in the future, the ability to precisely align reflection gratings needs to be demonstrated. The Water Recovery X-ray Rocket (WRXR), a soft X-ray spectrometer that successfully launched in April 2018 from the Kwajalein Atoll, required co-aligned X-ray reflection gratings. WRXR was designed to produce a moderate-resolution spectrum of the Vela supernova remnant over a large field-of-view. The grating module was manufactured, integrated onto the rocket payload, passed environmental testing and was successfully launched and recovered. This paper describes the grating and mirror alignment methodologies for WRXR, and their inherent systematic uncertainties. Improvements to the alignment method that are required to meet the tighter alignment tolerances of future X-ray spectrometers are also discussed.