I am also struggling with ideas about how to present the 2000+ stories and make it easy for readers to find. If anyone has any thoughts on this, feel free to email me.
My other suggestion in the first post, (which was actually a request for a reinstatement of a feature) is still relevant. Can't we have those story list links placed on the main page? There's plenty of room in the left hand column.

Another suggestion: Pre-filtered Lists - For example, stories featuring Spanking, Slavery, Rape, Scat (Yuck!), etc. Those that constitute a distinct sub-genre. You'd have to define a default order, 'Most Recent' seems logical.