When I try to rename a file (by pressing enter, then changing the extension of the file), it pops up with an alert asking "Are you sure you want to change the extensions ... " and the old extension is selected in blue. I haven't found a keyboard shortcut for selecting the new extension from the popup alert. Is there a way? I need to rename dozens of files, and doing it all through the keyboard would be so much quicker than selecting this one alert with a mouse.
You can disable the prompt under Finder's Preferences (see picture below):
This might save you some time if you are renaming multiple files. Additionally, you may want to look at Rename. It is a free utility that should serve you well for such simple batch renaming.