You are not using the most recent Zen Cart version.

the search box that you have is displaying correctly as this is the "SideBox" search function. You can disable it in your admin > tools > layout boxes controller > and look for the 'search' that you currently have in the right column and disable it.

The main search that normally appears in the header is one that you have eliminated somewhere in the code when replacing your header. Find the code and include with your header.

Do not throw away the css file, adjust the entries to achieve the desired look.