basically I need to use the scripts at verify.php. however when I navigate to mysite.com/verify.php, wordpress page shows up and throws 404.
I need to send AJAX post to this file from jQuery in the main wordpress index page.
As well as in the future I will have some more somescript.php to load via URL and I need wordpress to not throw 404.
You can create a custom page template. Within the custom page template you can include your own php code.