V5 is now downloaded

Is there an upgrade procedure, that will keep my settings, and get rid of the old installed version 4.6.3, and all its installed extras ?

there are no procedures that will keep all settings and remove all files that came with 4.6.3.
You may install 5.0 over 4.6 and most of the settings will remain, but some files from 4.6 will remain too.

Just install it and it will keep your settings. To make sure I backed-up all of the .cfg files from the PHPEd folder first, but thankfully I didn't need to restore them as it kept them anyway. All it lost were the 'recent files' history, the account settings, layout, etc, all remained.