There are actually two issues with larger pages.
The first is that saving an image of a page that has more than 32767 pixels in either direction causes issues. Weird issues. Particularly, if you open the image in Paint and try to scroll to the bottom, the program will appear to teleport between 32767 and the bottom. It looks as though the .png file has the correct dimensions, but everything after that point is completely transparent.
I took a look at the source and since you do not reference any apparent hardcoded limits, it would seem to be a limitation of an HTML canvas and I'm not sure if you could correct it without some multiple canvas trickery or something of that nature. It might also be helpful to communicate that there is a limitation to an end user or something, but that's obviously not my choice to make.
The second issue is that the max width calculation is a bit .. off sometimes. I'm considerably less sure about how this one works. I think it might have something to do with a <blockquote> element that has content that forces it to be bigger than, say, the container element of table would normally make it. For example, on a forum. Firefox seems to process this width correctly and gives you a horizontal scrollbar, but Adbuction refuses to go past a certain point in this scenario. I don't have any specific example pages for this one though. Sorry.
I'd like to close by thanking you very much for your time and effort - Abduction is a great extension.
Unfortunately, this is probably not going to be fixed in any meaningful way, I don't think it's possible to stitch together multiple canvas outputs into one PNG file.
About the only thing I can think to do is limit the maximum size of the drawing marker, or perhaps add a visual queue when it is too large to save.