I managed to fix that error earlier – add this to wpmu/.htaccess above line 17:
rewritecond %{REQUEST_URI} !index\.php
It should appear above the following two lines:
RewriteCond /var/www/wpmu/blogs/%{1} -d
RewriteRule ^(.+[^/])$ URL/$1/ [R,L]

Before you change the .htacess file, go to
http://yourdomain/wpmu/index.php and you’ll see it redirect to index.php/ – that’s what caused the redirection error. There’s still an error if you go to wpmu/wp-admin/ but if you go to wpmu/main/wp-admin/ it’s fine.
Version 0.1.1 is likely in a day or two!