Okay. It was the simplest thing to try first, though I wasn't expecting a miricle. 🙂
You mention that you've already replaced all of the fonts on the system with known good copies, so I think that takes the fonts themselves out of the picture.
The other common problem in an upgrade over an existing OS is Font Book's database getting trashed.
Restart and immediately hold down the Shift key to start into Safe Mode. You can let go of the Shift key when you see the progress bar towards the bottom of the initial gray screen. You will be asked to login. When it finishes booting to the desktop, restart again normally.
This clears all cache files from the user account you log into in Safe Mode. More importantly, it clears Font Book's database.
Do not launch Font Book yet!
If you have any third party fonts in the /Library/Fonts/ folder, or the Fonts folder in your user account, move them out to a new folder on the desktop. Now launch Font Book so it can create a new database based only on the fonts supplied with the OS.
What happens now?