So I want to get rid of these grey boxes that got added to everything in the overview. They are in the bar as shown in the image, they are in every text in the overview search as well.
For my taste it is disgustingly ugly. And I can't find where I can make it go back to normal.
Oof Manjaro loves to add some... tasteless additions. The shell theme is definitely your problem.
IMO the only non-stock shell theme that's acceptable is Ubuntu's Yaru as it has been tested for accessibility and contrast, and is 100% supported by Canonical.