The shortcut Icon's on your Dock can be replaced in a couple of ways.
1. Open your Applications folder in Finder, click hold and drag the Icon from there back onto your Dock.
2. Open your Application folder and open the Application from there. Then control (right) click on the new Applications Icon in the Dock, select Options, then select Keep in Dock.
As for those Applications that do not open.
1. Make sure that you are logged into either your Admin. Account or a Guest User Account that has permission to use those Applications.
2. If you have upgraded to say Yosemite 10.10 from Snow Leopard 10.6.8, then you will also need to replace those old Microsoft app's as well.