This is a very interesting idea for a movie, but you should pay attention to these details:
-When making a stop-motion, make sure to do it in a place where the illumination don't changes every time. Like, next time you should close your windows and turn on the room's lights.
-For let scenes more enjoyable, add some more life, like in the 3D animation part. You could, for example, put some tall grass or some critters to add more life.
-When making a transition like "10 minutes later" or "30 seconds later", be sure you can make use of a long time of a action. For example, for he getting at the duck, you could make he get faster by making he take the line off from the toolbar. In the duck scene, you could have made him press the copy button very fast for a more comedic scene.
Other than that, it's a very cool short. Good luck on the next works!