I'm merging 5 photos using the PS Camera Raw merge. The ground is fine in the merge but the sky is a bit pixelated. I'm thinking this is because the sky changes slightly between the shots. Can anyone recommend a workaround?
A RAW overexposed - that's badly set camera! I guess the image sensor in your camera is a bit smaller than full 35mm and you didn't check the exposure. Small sensor cameras have much less room for lousy settings than bigger ones.
If the camera allows exposure bracketing learn to use it in the next flights. You must take more shots, but the film costs are not a problem of today.
But assuming you cannot do a new flight you must replace the overexposed sky with something less disturbing. Of course the result a lie, but hopefully this is for leisure, not for anything critical where edits are forbidden.
Increase the canvas height to a square. Insert a new layer. Select the foreground and background color from the non-overexposed sky. You need blue and grey cloud.
Fill the new layer with Filter > Render > Clouds. Squeeze the rendering vertically to to the height of the original sky area to get more flat clouds:
Make a selection and cut a piece of the rendered sky. Paste it in place as a new layer. Close the rendered sky layer:
The selection was made with magic wand and it's not accurate enough except in small size and on the screen. You must learn how to make more precise selections. You must walk through the edge with big zoom and draw the new selection bit by bit.There's no shortcut for the job, but fortunately you can fully utilize background removal tutorials.