As I understand this correct: You want create a popup window in the moment you click on a link. THis popup window shall process some data and change the window url of the opener window and close itself after it? If so, thats easy ^^
The easiest way is to give each window a name. Then you can call them by their names and work with them like any other JS object.
Another way is to use the "opener" reference. Each new window opened with the "open()" function have an opener reference. So you can access it and change its location value and close the popup via "this.close()". Thats all