I haven't actually lost the comments -- they're all archived at my new DISQUS commenting system, but for some reason when exporting the comments from JS-Kit/Haloscan, everything went into ONE folder (the "Bedbugs Comments" folder) so that comments don't appear in their respective threads.
I'm considering ways of remedying this (if anyone has dealt with this problem in the past let me know!) the least drastic being figuring out a way to get an XML file that Disqus recognizes as having individual thread information for each comment, the most drastic being uploading BY HAND every single effing comment that's ever been made on the blog. Which I'll do if I need to but it's an absolute last resort.
In the meantime, I have the old Blogger format -- with terrible JS-Kit commenting system -- intact (that will still provide access to every old Haloscan thread in its proper blog post). I can switch back and forth between the two at any time and I imagine fixing the problem will likely require me to do this. So please bear with me for all remaining technical difficulties.
For now, I'm keeping the Disqus system -- Disqus still isn't as easy as Haloscan was, but it's a huge improvement over the super-clunky JS-Kit, so for now you'll be able to comment through Disqus
EDIT: EUREKA! I was finally able to find the old Haloscan (not JS-Kit) XML files after all. Hurrah! However, not all comments have been re-aligned with their threads for some reason, so I'll likely be troubleshooting for a while longer.
EDIT 2: My EUREKA was premature (of course, of course), but I'm still working on it. Any help would be super-appreciated.