I forgot to address your question about 300 files directly. What i meant to say was, if you learn the basics of databases, including how to design them properly by normalization, then you should end up with a set of database tables (a few system level files?) that can store/retrieve/represent a much larger set of HTML tables, as long as you can correctly abstract/normalize the common facts about those tables.
The MySQL book is good....if you want to learn practical mysql (in perl) as well as getting your breakfast of database concepts and basic SQL.
the hardest line to type correctly is: stty erase ^H