How to efficiently separate a stack of layered images into individual files?

From Lightroom a group of photos were "Open as layers in Photoshop."  The layers were all highlighted and I used Edit > Auto Align Layers.  Now each layer has been adjusted.  I would like to save individually each of the layers that has been adjusted as a separate image. 

    Right now, I can, starting at the top, flatten the layers, Save As, then in history unflatten, then delete the top layer.  Now do it all over again: flatten, Save As, unflatten, delete top layer., etc., etc. Since there can be dozens of layers, is there any efficient way to separate each layer into an individual image?

    If you're curious, these many images come from a focus stack.   I know that Photoshop can do Auto Align and make a composite image, but for that type of work Zerene of Helicon is definitely superior.  However, Photoshop is stronger in aligning severely misaligned frames.  Once Photoshop does the alignment (better than Zerene and Helicon), I'd like to be able to save the individual aligned images, then send them to Zerene or Helicon for the final composite

   Thanks for your help.

Lester.