Whenever dismantling something that you have never worked on before or don't have manuals and diagrams of, its always a good idea to take pictures and to number or mark parts so you can put them back together the way it they were before you started. From what you've described, its possible you have assembled the flywheel incorrectly. Drop the box, inspect for damage, take a good look at the flywheel while turning the engine over by hand. Google for pics or manuals.