If the properties of the user control are exposed with getters and setters, then they should be available to JS using dot notation. Give the control an ID and you can use document.getElementById(id).prop.
If in your situation you have 1-n results of which many can be selected, this will require a mechanism to maintain selection state, especially if the results are paginated (you don’t want an item selected on page one, have the user move to page two, and then go back to page one to find that the item is no longer selected).
I typically create an array that I will scan to add items when selected and remove items when deselected. I would then expose that array/collection/whatever as a property of the control, and access it as above.
If you opened the popup window using window.open and both Popup.aspx and Default.aspx are on the same domain, using the window handle you can capture an event in the popup window’s DOM from the context of Default.aspx, and pass it a reference to a handler that runs in Default.aspx.
Attach an event to the selection of an item or the unload event of the window or the control (something that signifies that you are done with the window, but before the control is removed from memory and its properties are no longer accessible), and pass the array of GUIDs to the handler.
That’s what I would try first.