[SalesForce] The VF page is in a pop up window. When the Case is created I want the parent window to redirect to the newly created Case

1 -> add a function in your inline page that executes window.parent.location=

function refreshParent(){
     window.parent.location='URL';
}

2 -> In the popup execute

window.opener.refreshParent()

rather than trying to refresh directly from the popup?

It's not best practice to interfer with this salesforce internal markup. Reason is that for all this you risk that salesforce updates might break your code.

This caveat emptor expressed I actually like to play with internals and changes in VF/markup where rare in the last years. With focus on lightning they might become even rarer.

Your problem could be that you're attaching the event too early (e.g. in $(document).ready) and the hidden fields simply don't exist at that time.

You could attach handler on somthing existent and try to trace the event until they finally reach the hidden fields. Or create a timer with setInterval looking for fresh created hidden fiels. Or reverse engineer the sfdc.js and even extend/override some of it's methods. I've done this for crazy things but can't recommend it for your use case. Simply because it's more effort and you'll end up with a more fragile result.

So better clamp teeth and go for the custom picker where you control everything. To loose the standard picker isn't too sad: take the chance and improve the user experience e.g. by autocompletes as you type, better searching capabilities or better doublette handling.