Hi Chris,
These could be a configuration problem and not malware. In some cases, it would be a line in the .htaccess file, but there could be other causes too. If you know where to find the error log for your site, it should have details on what caused the "500" error instead of the expected "404" page. (The hosting company can help you find the error log, if you're not sure where it is.)
If you had an infection in any of the theme files, you might want to try reinstalling the theme, in case any the files are missing or still damaged (possibly including the file that generates the 404 pages, which might be the reason for the error).
-Matt R