After your done painting, clear coating and such, let the paint cure for two weeks or so and then go ahead and reassemble. After that period of time the paint should be much more resistant to dings and scratches, so reassembly should be easier.
As for the order things should be put back together, I'm not sure I can help there. Personally, I don't think it matters much. Just put things together in an order that makes sense.
As for the order things should be put back together, I'm not sure I can help there. Personally, I don't think it matters much. Just put things together in an order that makes sense.