Thanks for sending sample files.
1. The Gerber files actually look fine. Some PCB manufacturers who use older CAM software have troubles viewing Polygons and Composites. Perhaps you can send your sample Gerber files to another board shop just to get their opinion if they can view the Gerbers. Your file are not standard stuff that a normal PCB designer would send, but they are Gerber and drill.
2. For the Oval Hole just add a Drilled Slot in FAB 3000. You can put FAB 3000 in NC mode (menu: Windows / NC Mode), and the Add the Drill slot in the menu "Add".