The shift of icons and windows on the other screen is caused by Windows.
As for the aspect ratio, all I can say is try setting your desktop resolution to the game resolution and enabling aspect ratio preservation there. Then you can change it back to native.
Or have your monitor do the scaling, and set that to preserve aspect ratio.
If your icons aren't moving back properly, look for a utility to save and restore their positions. I've been using a 64-bit port of Richter's Desktop Icon Position Saver for a while now, though I had to modify and rebuild it to get it working properly.