How to keyframe a crop in Premiere Pro CC
Before I start I'd like to mention that this would be much easier in After Effects. If you plan on doing this more often, you should consider learning AE to be able to do things like that faster.

So, to follow your approach I created a transparent layer, put the timecode effect on it and cropped it using the crop effect. It looks like this right now:



Since you want to resize and move it, you'll need to activate the animation for two parameters in the effects panel: The "size" parameter of the timecode effect and the "position" parameter under the motion effect (which is applied to each clip by default). You can do this by clicking the clock symbol next to the parameters name (see the next image). Make sure that your playhead (in the timeline) is at position 00:00, since activating the animation will create a keyframe at the current position.



Now, move the playhead to the point where you want the animation to end (i.e. the timecode has arrived at your desired position and size). First, alter the percentage value of the "size" parameter of the Timecode effect. A keyframe will automatically be created (see the small diamond shape in the timeline next to the effect settings panel). Then, adjust the "position" parameter of the motion effect. Again, a keyframe will automatically created. Adjust both parameters until you're happy with size and position. Then you're basically done.