Heh, that's an interesting issue.

Could you have photographed the scene using, say, portrait orientation of the camera so as to have included some detail in each image for Photomerge to "bite" on down at the bottom?  I actually did a sequence not long ago just that way.  There's a lot of sky at the top but I had enough ground in each image to get a good Photomerge result.  Even a wide angle shot of the whole area in addition to your individual exposures can be useful, and it's surprising how well Photomerge can put things together; I've actually made multiple shot stitches successfully with two different focal lengths.

For this set you could Photomerge the parts with detail,then overlay (underlay) the remaining frames and move them around by hand, and fine tune the blending with curves etc.   Since sky isn't much but gradients you have a lot of flexibility - even to the point of making up parts of the sky with gradients, though you'll have to be careful to match color (and possibly remnant noise) so it doesn't look weird. 

Oh, and when you think you've got the color all matched up, look at each individual channel.  That can reveal slight mismatches.

-Noel

Clear skies can be a problem for most stitching software, I gave up on Photoshop in favor of Autopano Pro - much more efficient in stitching multi-row panos. Well it is a dedicate program

But here is a little tip from Doctor Mike. Open your images in Photoshop and put a series of black blobs in the sky - these will be markers. You need to put them in the same place in every image - I use roughly a 20% image overlap. Then take your images into Photomerge or other pano software and stitch. Once done, just clone them out. Works for me - but you need to ensure the "blobs" are in the appropriate position on each image.

Hope this helps

Mike