Probably the best thing to do is to reinstall com_biblestudy. You don't have uninstall, you can just reinstall right over the top. That should put back the files you changed.
As far as why its running slowly, it totally depends on what changes you made. There are a number of dependences beyond just the view and template php files involving the model and other mysql queries so its not a good idea to make those kinds of changes.
On the other hand, if there is a feature you'd like to see, let me know and we'll see if we can introduce it into a future version.
Blessings,
Tom