Sounds more like you needed to read a book about mysql + database design. Its good to come up with workable solutions using what you know. Its better to figure out what you need to know for a great solution and go learn that.
That's my philosophy anyway. And I would imagine reading just enough to know whether you really should start from scratch again, or read much more to grok the required intricacies, would be worth it.
I'll try to put together some reproducible code, but for example I had a relationship table that once it grew into millions of entries, took noticeable wall-time to simply access via a primary key. Switching to InnoDB after spotting a note in the memcache FAQ that it supports much faster primary key fetches fixed that, but before that I was looking into the black box with no good leads on fixing it.