Unfortunately, without knowing what you "tinkered" with it's hard to say what to replace without things getting hosed further...
You should be alright with uploading stock versions of everything but the /includes folder and the /styles/wrapper.inc.php file (if you've made custom islands you'll want to back them up from the /cache_builders/custom/ folder)...
This is also why modifications to the stock files are unsupported, were have no clue what the end user changes and how those changes affect the forums.
