The 404 error is a case sensitivity issue. I think the user profile page has Login.php instead of login.php. It is probably just a matter of finding and replacing the link.
Most likely so is the verificationi issue, but I'm not quite clear on what exactly you are describing... are you saying when you register a user from the admin section it isn't sending the verification email? or when you send the verification email the link doesn't verify properly? My best guess is another case sensitivity issue, but I'd like to hear more details so that I can make sure.