Mike, it's a tough situation. It's so important that you are informed about your site and holding an agency (or any partner) accountable is critical. It's tougher once the relationship is over and it is a big deal if you find out you got hosed. It's unfortunate that this wasn't caught earlier.
At the very least, they should be able to give you some sort of overview. I spent most of my career on the agency side and you paid for their services and asking for information on your account isn't out of line, IMHO.
If you can get the data, great, however you know enough to not let it stop you. I mean, if you can hold them accountable, OK, but that won't change your predicament, right?
It sounds like there's plenty of black hat stuff you need to clean up and are smart enough to know to make it a priority before it really hits your site negatively.
And you know for next time -if there is a next time - who not to go to or what to make sure no outside partner does 
Good luck!