I use PTGui, so I can only really comment on your issues from the PTGui toolset point of view. You are basically stitching a 3-shot pano, with multiple images taken for the same segment of the 3-shot composite. If you do not move the camera at all during or between each successive shot at a particular pano segment, then you can perform the initial 3-shot stitch and then swap in other images and regenerate the RENDERING of the pano composite, without restitching. You can also do the initial stitch and then make a template of the stitch, capturing the stitch parameters, etc., and then apply the template to a new set of images to create the exact same stitch from a set of 3 new images.
For example, let's say you took 5 shots at each of 3 pano positions for a total of 15 shots. You look through all of the shots and decide there are elements in all 15 shots that you have to have in your final composite. Presumably, you shot your images by placing the camera at position 1 and shooting images 1-5, then panned the camera to position 2 and shot images 6-10 and then panned to position 3 and shot images 11-15. The result is, that there are no contemporaneous images across all three pano positions, meaning that the images that you combine from positions 1, 2 and 3 to make a pano don't really matter that much.
Choose your best image from each position and then stitch them. Take your time to get the stitch correct, and constrain the stitch with the horizontal and vertical line tools in PTGui if need be. Once you render the stitch and refine it to your liking, including your choice of projection, make your "Master" full res stitch from this pano. Save the stitch as a Template in PTGui.
Now you can bring in your next three images - most likely, the next best three across the pano - and apply the template to them and render the full res version, version A, of this pano. You can layer this pano on top of the Master in PS and reveal the portions of version A that you like, sending it into the Master. Repeat for versions B, C, D so that you will have 5 layered panos in PS that you can blend together. The one thing that will remain consistent is the optical and perspective correction that the stitcher applied and the projection of the resulting pano images. Each pano will be identically registered with the others, so the blending should be easy peasy. If you decide to change projections, you will have to regenerate the panos, but you can save each one as its own "project" in PTGui and just change the projection and re-render as a batch in the batch renderer.
PTGui also has a masking function that permits blending inside PTGui prior to the final rendering. The masking tools may not be robust enough for what you are doing though. Finally, PTGui can render to a flat document, or a layered document - that is, you can render each f the above panos into a PSD that has all of the layering of each segment intact, similar to your layering approach in PS.
This workflow is one way to, hopefully, save you the hassle of trying to align and correct everything on an ad hoc basis and let you get to the "art" side of the composite more efficiently.
Have fun! I like the concept you developed in the thumbnail of the "final" version of your correction.
kirk