So far I'm scribbling (mentally) a short list of how this thing's going to work. I'm planning to actually write several command-line scripts that do the dirty deeds, then write a Perl/Tk interface that ties them all together. In the spirit of "90% of any Perl application is already written", though, I'm doing my best to pick modules that will make short work of this, before I set to the long work of trying to code anything.
Right now, I'm looking at LWP::Simple for grabbing the images, Image::Info for giving me basic stats about each one, and GD for generating the final product (with filling and smoothing to produce the illusion that all the panels were meant to be in one image.) The only functionality I haven't located yet is locating patterns (really basic stuff, intersections and junctions and corners) within the PNG file and then cutting it into pieces based on those patterns. I've found a script which matches patterns in a GIF file so far, but it would have to be extended a lot more, and I'd have to have a much better knowledge of PNG than I currently have.
Two options suggest themselves -- one, more searching and looking in an attempt to find out more about structures in PNG. Two, generate some PNGs from the JPGs that the strip's currently in and fart around with the raw data until I have a reasonable grasp of what's going on.
Option one seems much more palatable, but also (so far) less successful. Maybe I'll have to write a lot of code to make it work, and maybe it'll be useful code I can produce a module from.
Time will tell.