I talked to the service manager at my dealer and he said the only pieces that would not retain the factory warranty would be those that I replaced. However, if they deem the drop caused a failure of other parts they may not be covered. For instance, if a u-joint fails and they attribute it to a vibration caused by the drop it wouldn't be covered by the warranty. Fair enough, I guess it's the price of looking awesome!
I think I will go with a 3/5 drop initially since the drop is adjustable. One question that does come to mind is that you all mention changing shocks. Everything I've read says the kit comes with front struts and rear shock, do they not work well?