I am very confused by your posts. You first state that you using mojoPortal on Medium Trust on GoDaddy, you then state that you did not copy the contents of the /bin directory in the MySQL datalayer zip to the /bin of the site but that "you should" copy the contents of the /Setup directory in the MySQL datalayer zip and that you couldn't install the mysql-connector because you don't have .NET 1.1 on your PC. You don't need to install the mysql-connector and having .NET 1.1 on your PC is not of any concern as you are using GoDaddy for your hosting.
Finally, you state you "got it" but then say there is "No difference."
If you clarify whether or not you have your site working and if you do not what problems you are having and what steps you have followed, I may be able to help.