Hey, heh, yeah, that’d cause some confusion. The wrong file permissions are odd, did you use make install?
For the login issues that’ll be because 5.0.4 has changed a default to turn WebSecureCookies to on, which requires TLS for cookies. See RT 5.0.4 beta1 Available for Testing
You need to turn that off. Try adding Set($WebSecureCookies, 'off') to your RT_SiteConfig.pm file.
Cheers,
Andrew