For a variety of biometric cross-spectral tasks, Visible-Thermal (VT) facial pairs are used. However, due to a lack of calibration in the lab, photographic capture between two different sensors leads to severely misaligned pairs that can lead to poor results for person re-identification and generative AI. To solve this problem, we introduce our approach for VT image registration called Vista Morph. Unlike existing VT facial registration that requires manual, hand-crafted features for pixel matching and/or a supervised thermal reference, Vista Morph is completely unsupervised without the need for a reference. By learning the affine matrix through a Vision Transformer (ViT)-based Spatial Transformer Network (STN) and Generative Adversarial Networks (GAN), Vista Morph successfully aligns facial and non-facial VT images. Our approach learns warps in Hard, No, and Low-light visual settings and is robust to geometric perturbations and erasure at test time. We conduct a downstream generative AI task to show that registering training data with Vista Morph improves subject identity of generated thermal faces when performing V2T image translation.