Thanks for the info! And ouch, regarding USB 3.0 SDHC card readers...
Separately, did you consider trying other stitching software, like PTGui Pro - or have done for smaller shoots? It seems, at least in the past, that PTGui used to be an order of magnitude faster with similar feature support and results as Autopano Giga.
That said, Autopano Giga directly supports graphics processor acceleration, which I am not sure PTGui can on Mac. Did you take advantage of this feature?
I have used PtGui since 2004, It is great software. But it is not suitable for stitching panoramas containing thousands of images for various reasons.
I did try it with a set of 12600 images and it failed to detect control points on a few hundred images, so this was a no-go.
Autopano Giga supports GPU to some extent, but not for much, really. Mostly for some display stuff, but not for rendering or any other really heavy stuff (AFAIK).
Both Autopano and PTGui are really amazing programs, I like them both!
Note: USB 3 card readers (that we were able to buy) are not really "usb 3" :-(