1. I was wondering if I need to do anything after installation, do I need to delete any installation files on my server for security reasons?
2. I need to make my forum non viewable from the public and only let certain people able to view any part of the forum. I was thinking maybe a password could popup when the forum is loaded but again I need to have it so you cannot view any part of the forum (Topics, Categories)
1. No need to delete anything, there will be no security issues from keeping setup.asp, and it may be needed in the future.
2. You can set Require Registration to on, in Admin Options-> Main Configuration. Only registered members will get to see any info other than the login page. Then you can set Email Validation and Restrict Registration to on in Admin Options->Email Server Configuration. This will allow you to approve any requests made to join the forum.