The error is related to your server not being able to handle “Windows” formatted file (Some servers do this). There is nothing wrong with it though… I will send you another copy of the plugin where all the files are “UNIX” formatted and it should fix this issue.
Yes the membership plugin and the affiliate plugin can work together and share the same login credentials but this work needs to be done manually at the moment. I am in the process of adding this functionality in the settings menu so it can be enabled just by checking a checkbox.