My guess: 400 classes ~ 20 packages ~ 10 packages actually used
Those with experience can conceptualize 20 components in their head.
I agree that this company wants to keep you on board. So save some grief and contract someone with 5+ years experience to refactor/document. After 1 week, this person should be able to explain every class and it's purpose.
I started with PHP too before Java and I must say the learning curve was steep. But hang in there, you're on the right track. When you get to the point where you skim through the "teach yourself in 21 days" books and understand everything, then that's when you've arrived. Now you can start to learn Java