The issue is that each read notification has a separate background color, which also needs to be overridden. This should help in addition to your other changes
.user-menu .quick-access-panel .read {
background: transparent;
}
Similarly with the search input, there’s a separate background applied there that would need to be removed:
.search-menu .search-input, .search-menu-container .search-input {
background: transparent;
}
We have a guide that walks through making CSS changes like these that may help, Making custom CSS changes on your site