The mirror or prism alignment only affects what you think you are seeing, not the actual photograph which is the lens projecting light onto the film. The mirror cannot distort the image, especially because it is out of the way when the exposure is made. So it's either the pressure plate, lens mount, or lens. Of those it's easy to check the body, which I assume the OP has done, so my guess would be the lens and perhaps an element has shifted or not been seated properly if its been cleaned.
We don't even know the type of lens the OP was using and some aftermarket zooms can be pretty awful out of the box, and shooting wide open exaggerates the problems.