I bracketed 3 exposures for each part of a panorama, and then stitched 3 panoramas together, 1 at each exposure, using photoshop CC (probably called photomerge). I now have 3 different layers with panoramas that don't quite line up (either manually or with "align layers") because of minute differences in the merging/stitching process. Is there a way to line up on content in photoshop?
You have to approach the stitching in a different way. First you have to fuse the exposure for each brackets and stitch the single images together. For fusing exposure you can use some plugins like enfuse or photomatix in lightroom. The other way is to do a manual exposure blending using layer mask in Photoshop. There are software like ptgui will do a better job in panorama creation.