This actually belongs to the
General Modification Help section.
You have way too many nodes. Theoretically you only need five nodes for a simple vehicle with one seat and four wheels. Not every shape has to be attached to a (separate) node. It's enough when they are parented to the detail32 empty. Nor do you need a whole new object for every part/color/etc. The collision box should be fine like that. If it doesn't work, check if you got all the parents and names right.
[Edit]
It doesn't matter on what layers all the stuff is.
