First, let me apologize for blasting this forum with so many questions--I just like to reassemble my trains as accurately as possible, and there is no ultra-detailed manual on how to do this (wow, what an awesome book project!).
Anyway, here is one question: when I attach the manual reverse switch to the motor housing, and then the rod jutting out of the top of the train, the rod seems to knock against the shell, almost lifting it up, and I can't imagine that this is accurate and I am doing it correctly. Here are some photos to attempt to illustrate the problem.