Repetition is the key.
Beyond making tables/notecards/etc what helped me through the first 2 years was constantly thinking about it. Whenever I was studying/reading about a disease, I tried to remember what drug you'd use to treat it, and thought about why that drug would work for that condition.
By doing that, you link drugs to diseases, which helps you remember mechanisms as well as pathophysiology, because there's a good chance that the mechanism of the drug has something to do with what's going wrong. Then when you remember one thing you remember everything together in a nice big chunk of info.
It also lets you access the information in several different ways. Can't remember the pathophysiology of some disease? Well if you remember the drug you use to treat it and the mechanism of the drug, you might be able to piece together the pathophysiology. And vice versa, if you forget the mechanism but know the disease you use it for, you can use the pathophys to get to the mechanism.