Excellent work under terrible conditions, Serj.
For the filenames, I have a possible suggestion that might help move things along: If someone generates a list of, for example, MD5 hashes of every file, you can compare the hash values to the files you have. Wherever they match, rename one file to the next. (Create two hashes/associative arrays/whatever your language of choice calls'em, and insert each filename by key, then output "rename <garbled name> <original name>" for each MD5 value. Then run that file as a batch file or shell script, obviously depending on the operating system.)
I'll gladly volunteer on my end, but I've renamed a lot of files for consistency's sake--usually, that means simplifying the title ("Hit" rather than "Hit Comics"), removing the dates and company name, and often the scanner's name--so it might be smarter to use someone else's archive.
Again, thanks for getting this back into shape. I don't even want to think about how much time it must've taken to rebuild!