Hi,
As Sushant hat mentioned there is now an internal discussion going on if and how the loading animation can be kept going during long-running scripts.
For your second question regarding the ability of updating labels synchonously while a script is running you have to directly manipulate the DOM elements of the page. For instance this worked for me: document.getElementById("M0:U:::9:62").textContent = "changed"';
You should be able to find the DOM Id through the develoment tools of your browser and in the case of custom fields there is a good chance that the DOM ID is the same as the scripting ID.
Cheers,
Clemens