Hello @ActorMike,
I can see that you have added this custom CSS:
.x-navbar, .x-navbar .sub-menu {
background-color: hsla(210,29%,24%,0) !important;
}
.x-navbar .desktop .x-nav > li > a {
background-color: rgba(9,33,77,0.65);
font-size: 20px;
padding: 20px 0px 0px 0px;
text-shadow: 2px 2px #000000;
}
The code above you have added has created a background color for the navigation menu items only. By default, the search icon do not have a padding on the right so that it will be aligned with the elements on the topbar and in the section area. You will have to add additional custom CSS to be able to resolve the padding. Using your browser’s Development Tool, you can check the live HTML code and find which CSS selector you need to use or what CSS code has been used to style the page.
Check out this video demonstration:

Dev Tools demo
In your case, you may have something like this:
So, you can copy the circled CSS code on the right side and change the right padding value from 0
to 10
pixels.
As for the Classic Counters, a fix has already been made. We do not have an ETA for the next update release though. You may need to watch out for the rolling out of the next update.
Hope this helps.