> [edit]: flake8, remarkably, dropped roughly an order of magnitude in performance between version 2 and 3. So that didn't help.
Sorry for the drive by, but did you try bisecting the flake8 change that slowed it down? Unless there were thousands of commits between releases, it would only take <10 runs to bisect, an automated bisect should be under an hour with a test case that takes a few minutes. Could be an interesting thing to try?