Revisiting this, as it seems I neglected @mouser's response (apologies for this), I believe I posted this originally when I was really busy, and never really returned back to see what the answer was.

So, mouser, to answer your question - all of it: the #1 and #2 automatic detection - when these work, it's awesome!. And all of the manual tweaking and setting of margins is fantastic when the automatic detection don't work.

I use the editor manually today (with it's great drag and drop stitching), but moving a notch by single pixels is rather uncomfortable compared to how the final step of the scrolling capture tool.

So - what I would really like to see, this final step as a standalone action/application that can be fed a png/jpeg.

[Promise to keep a closer eye for a response this time :)]

I cannot express how useful Screenshot Captor is to my life. (I believe it's time to add some donation money  :))

Anyway, my love today is director to the Scrolling window cropping step (the last step of the scrolling capture).
I would really like to see this as a 'standalone step'.

Why would this be useful you ask? Good question.

I use remote control sessions quite a lot - and take screenshots while on those sessions.
This introduces 2 limitations:

• Time - I collect screenshots to preserve time, and have a 'local view' of what I saw remotely.
  For this reason I have SC setup to save the capture automatically without interfering or asking what to do with the capture.
  
• The 'object' of interest is remote, embedded in the local 'remote session' window.
  This means that SC can't 'pick out' the region out of a 'flat image' (which is the remote session).

After the session is over, I summarize my thoughts/findings and make use of the screenshots.

For remote scrolling content, I've made it a habit to use the "Grab selected Region" option, followed by the "Grab Repeat last size+pos" and grab multiple images at the same location (after scrolling manually).
Later, using the excellent drap-n-drop option in the editor window, I combine them into a single scrolling capture, and I manually "Splice Out" with the SpecialFX2 menu item.

If I cold launch the Scrolling window cropping wizard on the combined file, it would make this process a lot faster.

Can the scrolling window cropping wizard be launched explicitly? (I searched the forum, but couldn't find information about this)
If so how?
If not, I'd love to see this as an update.

Thanks mouser for a fantastic tool.