On the Mirador dark theme:
You’d set the dark theme originally by editing some files. I suspect that you’ve now overwritten them with the originals as part of the upgrade process, so you’d just need to go make the same changes again.
On the error message:
I don’t think that’s either Freedom or the Mirador viewer. If you notice when scrolling down the page, underneath the working Mirador, you have the Universal Viewer also on the page, and it seems that’s what’s throwing the error.