Kyle – I’m going to email you, but to address some of your points:
Follow the instructions given on that page to chmod the files and directories. It’s for your own security.
Michel_v has pointed out that WPMU uses dashes in mysql table names and this may cause problems in some situations.
Your confusion about the table names is understandable – the installer should create tables called $prefix_main_* to support multiple blogs in the one database. I’ll have to look at that for the next release.