Plugin's add nav tabs but when plugin removed they stay?

Ive been testing a few of the plug-ins on this site and they are all great and well thoughout. My only issues with it were that coming from the simplicity of the option in WP to automatically install plug-in to having to download and manually upload these via ftp whilst following the instructions they do not appear in the plug-in install area and as such when coming to remove them I just deleted the .php file from the directory.

An issue I have found is that I installed the 'blogs directory' and the 'global site tags' plugins but found I already had these bundled in my original install so this created duplicate tabs in the top navigation so I quickly removed (deleted the original plugin PHP files from the directory) but these tabs remain and they are not found in the header.php file (where I edited them in the past?!?!).

Can you please let me know where I can now remove these?

Thanks

James