Sizing all layers to match

You don't necessarily need to make them all the same size. The biggest issue seems to be that the layers have some opacity that makes the parts that aren't aligned noticeable. To address that, you could add a solid white or gray background. I can see that there's a black Background layer with the visibility turned off-you could fill it with white or gray to make the cloud areas show through. 

Then you could select all the layers that make up the background texture (the semi-transparent clouds and the solid color). You might group them, duplicate the group, merge the layers in one group, convert the other group into a Smart Object, and hide the Smart Object (but keep it as a backup). 

Then you could crop the image so that the overlapping area isn't noticeable. 

If you want more margin around the image, you could use the Crop Tool's Generative Expand option in the Options bar (Window > Options).