Check out the train simulation I did in CATIA V5 with the DMU Kinematics workbench! Your assembly literally has to be perfect before you can even begin to attempt kinematic simulations. Which is why I often times assemble a few pieces and then simulate a small portion of whatever it is I am building just to make sure it is working, then I add on a little more and repeat. It takes longer but is easier to diagnosis problems this way. I use an Excel spreadsheet to help me keep track of the number of degrees of freedom of each part that is not fully constrained during assembly. This seems to help me a lot. What are your strategies?