Since the ‘timer’ has to execute on the client side, then you will need to find some JavaScript that will ‘run’ the timer and pop up the box.
You can’t do this with PHP code (WP filters, hooks, themes, plugins), because PHP runs on the server, not the browser.
Browser side stuff has to be done with JavaScript…and the client (visitor’s browser) needs to have JavaScript enabled. (Although you could create a plugin that runs the JavaScript code on all pages…)
But the solution is some client-side JavaScript code.
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