I've been doing a number of panoramas of a flat barren landscapes lately, but I have been running into issues with a wavy horizon. I can remedy this to a certain degree in Photoshop with cloning but surely there must be a better way to fix the geometry/projection. I love the convenience of doing panoramas in Lightroom and getting a DNG output to work with afterwards. Is there a way by means of a plugin or otherwise to correct this in Lightroom itself? If not, please recommend efficient Photoshop methods.
Check that your camera is level in pitch and roll.
These types of issues happen when you shift the orientation/location of the camera between shots. The bumps typically happen at the seams between member images, and the changed orientation caused misalignment.
Do not rely on a level on a tripod, especially if you're using a ballhead, as that typically only tells you if the legs are level. A 3-axis hotshoe spirit level can come in handy for this. You may also want to do a little research into rotating around the no-parallax point of your lens, but with this kind of scene, that's unlikely to be the problem.
Suck it up. Don't use Photoshop or Lightroom to stitch.
Use a real panorama stitching package, such as Hugin or PTGui. The reason for this is that Photoshop's photomerge, while a good basic panostitcher, doesn't give you a whole lot of control to correct stitching errors like this. Specialized panorama stitchers do. Both Hugin and PTGui can let you set individual image parameters for pitch and roll.
Both Hugin and PTGui also have "preview" modes, where you can drag to correct horizons. Dragging vertically corrects for pitch, dragging horizontally corrects for yaw, and right-dragging corrects for roll. This is a very fast and convenient way to correct for bowed or s-horizons in stitched panoramas. And you can also correct for mismatched control points, as well as mask specific portions of member images, to achieve smoother seams when parallax error interferes with a clean stitch.
Are you using LR CC? Have you tried boundary warp?
I think the wavy lines are caused by distortion from your lens before the photos are stitched. Do you apply lens corrections to the images before stitching in LR?