1) User registration uses the webassist/plugins/registration/registration.php (or webassist/plugins/registration/full/registration.php if you select the option in the admin to use the longer registration form.
the user profile uses the users_profile.php page.
2) All of the emails use the tempalte files found in the webassist/WA_UniversalEmail/Templates/ folder.
Users can see ther orders on the orders_detail.php and orders_history.php pages.
the admin can manage the orders on the pages in the admin folder whose names begin with "orders_"