When taking images of some occluded content, one is often faced with the problem that every individual image frame contains unwanted artifacts, but a collection of images contains all relevant information if properly aligned and aggregated. In this paper, we attempt to build a deep learning pipeline that simultaneously aligns a sequence of distorted images and reconstructs them. We create a dataset that contains images with image distortions, such as lighting, specularities, shadows, and occlusion. We create perspective distortions with corresponding ground-truth homographies as labels. We use our dataset to train Swin transformer models to analyze sequential image data. The attention maps enable the model to detect relevant image content and differentiate it from outliers and artifacts. We further explore using neural feature maps as alternatives to classical key point detectors. The feature maps of trained convolutional layers provide dense image descriptors that can be used to find point correspondences between images. We utilize this to compute coarse image alignments and explore its limitations.