Here is a schematic view of the 42 images I used for the pano in the first post.
Columns A through F show the various panels. Rows 1 to 3, rows 3 to 6, and rows 7 to 9 represent HDR bracket sets shot at different focus planes.
So for panels A to D I shot 2 focus planes. For panels E and F I shot 3 focus planes. Rows 1 to 3 is the nearby focus plane, rows below those are more distant. Each focus plane consists of a set of 3 bracketed images. On E and F I added a third focus plane to guarantee a sharp bush image, it was rather close.
I would have preferred 4 or 5 focus planes for this shot, but there was not enough time in this case, the sunset was fading fast.
The basic workflow was to import rows 4, 5 and 6, A to F into Lightroom as a sort of "average" HDR set. Those are the HDR bracket sets exposed for infinity.
I developed the single image at row 4, column D as best I could, then sync'd those development settings to its bracket set below in column D, rows 5 and 6. There was a lot of back and forth here with exporting the bracket sets to Photomatix to optimize the settings for a good HDR image. And I did a lot of exporting of just row 4, A to F to Photoshop's Photomerge to test for color and tonal consistency from panel to panel.
Then I imported the rest of the images into Lightroom and applied the finalized row 4 development settings vertically up and down the columns using Lightroom's Sync function. Row 4D had the brightest areas, that's why I picked it as the standard.
Then I exported all the images to a folder as 16 bit TIFs. I used the batch function in Photomatix to process all the HDR images, taking three at a time.
When Photomatix was done, things were crunched down to HDR composites, 2 images each for columns A through D, and 3 images each for columns E to F. All the HDR images represented different focus planes.
Then I manually processed each of the column A through F focus stacks in Helicon Focus. That was a lot of work! Manual mode was OK because so I had the opportunity to correct issues with moving clouds and plants using Helicon's built in layer masking functions. Note that AFAIK only the Professional and 64bit versions of Helicon have the masked editing feature, and it's worth it.
Then it was just a matter of stitching and a bit of post processing. Piece o' cake!
If anybody notices that I am missing useful automation steps, please let me know! There are a few steps above where Lightroom has export and automation features that would be very useful...except they don't work in batch mode!
PS. Biggest newbie mistake is to try to stitch the individual focus planes and bracket sets, THEN do the HDR and focus blending steps on the stitches. That usually generates very interesting moire patterns. Always stitch last.