Is there a way to remove the transparency of the desktop panels, ie those I am using as the equivalent of the Windows taskbars?
I also want to set the colors, but there seems to be no way of doing it directly from the context menus.

What files are their settings kept in, can they be fixed directly there?

if you don't want transparency you'll need to use a different non-transparent desktop theme, or you can just change the theme used for just the panel in systemsettings -> workspace appearance -> desktop theme -> details -> panel background

for colors you'd need to change the appropriate svg file I think, searching the forum should explain it (I'm pretty sure this has been asked and answered)