First: Sorry about my slow reply.
The software for the HDR Focus Stacking works wonderfully. It took some getting used to, in terms of settings, but it isn't impossible. My next problem is configuring software to batch edit the focus stacked images, but I'm sure I'll find something...
As for the shooting of the HDR Focus Stacked panorama: could the focus that is selected be locked, and then made so that each time the shutter is pressed it takes the whole HDR Focus Stacked shots, rather than having to open the ML menu and select the focus stacking setting?
On to the bug: When the card is full, the waring 'Card full' pops up, but the camera continues to try and take photos until it's reached the end of the script. I guess there should be some kind of "is the card full" check. Maybe there could be a counter that checks too see how many shots are needed for the press of the shutter.
Example: a 3 shot HDR + 4 section focus stack is 12 total photos. If the camera can only take 10 photos, then ML will say that it can't take that one because there isn't space.
Of course, this wasn't world ending. I simply waited for it to end, I deleted the partial HDR Focus stacked section, and then copied down the settings I had. I did the last part, as I switched to a new ML card without the old settings. In the future I'll keep an eye on how many photos I can take... This is on a 16gb card, but I shoot in RAW, 3 shot HDR, 8 section focus stack, and around 50 sections on top of a previous HDR shoot.
(P.S. is there a way to get the settings to stay in the memory in between changing cards?)