Mister Epic, I just dumped the whole run using the latest version of Glide Napalm. I was able to get it to run after figuring out some more stuff. I recorded all the parts separately using Mupen's AVI dump feature, just like before. I am currently 7-zipping it all with my modified AviSynth script which puts it all together and adds a logo (of any size up to the video's size, centered without resizing) and subtitles. It would be great if you'd just replace the logo file and encode it. However, it's ~5.5GB and I don't know where I can upload it.
Note: I didn't use the weird things suggested in that thread you linked. I dumped my own way, which worked without desyncs, crashes, graphical glitches, or quality loss.
I'm uploading my dump to the space I have. When it's done, there'll be a 5.37GB 7z file containing the Yoshi's Story dump. When it's done uploading (which it's not yet, but will be in about 15 hours from the time of this edit), you'll be able to find it at http://lex.clansfx.co.uk/requested/lexcomicalflopystasdump.7z
Edit: I sent MisterEpic
an exact copy of my entire mupen64 directory and it works for him. I've cancelled the upload in the out-stricken paragraph above in favor of MisterEpic doing his own dump instead of having to download mine. :)