Well, for the drive boot prob, all you should need to do is go into the BIOS and specify your boot order which should help the computer know what drive to boot from first.
Try using another mouse in the computer? Just because you can use a remote desktop connection and have the mouse work only means that the computer youur sitting at has a mouse that is working.
You cam also go into the device manager an click the menu option to show hidden devices and get rid of any old devices that might be causing a conflict.
Little bit confused on the mouse troubleshooting though so if you can give me more info, maybe I can be of more help.
Can you try a new mouse, or one from another computer? Does the existing mouse not work in any other computers?