I really sounds to me like you are dealing with three different issues here.
This is most likely a matter of simply getting the correct path, and it can be a bit confusing given the way Dreamhost logs directories are set up (symlinks, etc.) It's hard to tell exactly what the problem is, as you did not include a snippet of exactly what path you used. My suggestion is to carefully explore the "logs" directory in your main user directory (/home/user/logs/), to find the appropriate location for WebLog Expert (I'm not familiar with that particular program) and try again. Alternately, you could post the path you used here, and we might be able to tell more about what is going on.
This looks like the natural result of your domain running a program where .htaccess based Apache re-write rules are interfering with urls that try to access your stats directory (WordPress, Drupal, Joomla!, etc.). This is easily enough fixed using information from this Dreamhost Wiki Article on mod_rewite or this Dreamhost Wiki Article on Making stats available with htaccess .
This could simply be a matter of confusion regarding which user name/password combination (webId, shell/ftp user, etc.) you should use (assuming of course, that there are not "UpPer/LOweR Case" or other common "login problem" issues). You can confirm the correct user/pass to use, or add new user/pass combinations from the Control Panel Site Statistics management page, by clicking on the "# users" link in the "Stats Users" column adjacent to the domain name in question. From there you can edit passwords, add additional users, etc.. Often, simply inspecting the "user" that is currently set up will indicate which user/pass you should use; you can always change the password there, or add another user/pass combination if the indicated user is not enough of a help to get the correct password to be accepted.