Comments are no longer broken
The title could have read, "Comments were broken for reasons having entirely to do with a small technical workaround your author made two years ago that broke during the MT4 upgrade because he didn't pay attention to a few filenames, but which has now been repaired."
Many thanks to the denizens of #movabletype on irc.freenode.net. They made me glad I actually paid for MT3.
Here's a test comment just to be sure.