There are two kinds of ProComp 6" lift kits - the stage 1 doesn't require near as much modification as the stage 2. Either way, it's going to be tough to get some things (like ball joints and cv axles) covered with such a big lift. But, baring this relatively cheap parts, expensive things like brake components, drive shafts, transfer cases, etc. will all still be covered.
I would suggest you talk to your local Toyota dealer and see if they recommend a local off-road shop. A lot of places are working with dealers now and guaranteeing their work.