1) That is actually described detailed on our installation page. It is simple as that. You don'T upload the folder you unzipped but its contents.
2) "Some server error" really does not help us to help you. We need the proper error message. Also of course it is an older version and we don't know if the installer you used works properly. Sorry.
3) Our jPlayer plugin supports webm but only as counter part formats (HTML5 vs FLASH fallback). So you need to have mp4 files first. You can only upload webm via FTP as otherwise you couldn't use them. This is explained on the jPlayer plugin documentation you can access via the admin backend of Zenphoto (not again that it is of course for the latest Zenphoto release).
I hope that helps so far.