I have exactly the same problem. I got around the ‘internal server’ error the same way by FTPing the file from Server A down locally and uploading to server B in the same place.
But I have had no joy in remedying the ‘incompatible archive’ error. I have tested and am able to clone server A and restore again over server A so this leads me to believe it is a difference in environment. Server A is a virtual server with multiple hosts on – of which we have only access to the htdocs folder for our site. Server B is a virtual server which we have complete control of and WP is installed under /var/www. Could it be that WP Clone tries to restore to the same folder paths? The servers have different flavours of Linux also.
I have spent too much time on this and am going to start looking at duplicator if I can’t get it solved.
