As the previous answer and comment have suggested, the normal way of doing this would be to put the code you want to run after the script loads in a function in setTimeout. If you are worried, for instance, about event handlers being triggered while you are waiting and causing an error, then you need to disable the event handlers (e.g. element.onclick = null) then re-enable them within the time-out function. I suppose you could also do something like this:

var pause = false;

...

callExternalScript();

pause = true;    

setTimeout(function() {

   pause = false;

}, 3000);

...

function oneOfMyOtherFunctions() {

    if (pause) return;

    ...

}

...

but this is messy because you have to include if (pause) return at the start of every function that you want to disable while the script is paused. Also you may or may not want to add extra code to run all those functions that were called while the script was paused, once it has been un-paused.