#1. Think of the spider like a Javascript disabled browser - the spider 'sees' your web-site like a browser, it cannot see pages that are not linked to. It has no access to your directory structure.
#2. Most links written from Javascript are unreadable, because the spider is not a Javascript engine, it doesn't know that your popup menu exists. See #3.
#3. Provide commented out links, or a 'site map' to help the spider. Eg. if your web-site does have a popup menu that uses Javascript, add hidden links like
<!--
href="page1.aspx"
href="page2.aspx"
-->
this won't affect users, but will match one of the spiders regex patterns. These hidden links can be generated by your code at runtime and added to the page.
#4. If the spider reports a problem such as 404 Not Found, or 401 Not Authorized then you should check the URL in a browser (for 404's), and also consult the Forms Authentication section (for 401's).
#5. If need be, by pass the spider and add documents directly using the DocumentIndex class's AddDocument method or manually with the Index Management tool.