With a 3D pen? The parts being not as smooth isn't likely your biggest problem. How do you propose to create parts with any accuracy? Rails have to be parallel and axes have to be perpendicular. I can't imagine trying to build anything like a printer with a pen. Maybe it's possible, but i wouldn't try it.

You'd be better off trying to find somebody over on reprap.org who will print you a set of parts for a reasonable rate. They have big hearts over there.