In general, it's as easy as adding the jQuery code within the appAPI.ready method's callback function in the extension.js file, as you mentioned. I tested your example using the following code on Win7/Chrome:
appAPI.ready(function($) {
$(":input").on("blur", function(e){ console.log(':input blur'); });
});
If this isn't working for you, I recommend opening a Crossrider support ticket (support@crossrider.com) specifying the extension id and we will be happy to investigate for you.
Disclaimer: I am a Crossrider employee.