I would think that the suspension components would NOT be covered if you lift your 4runner. Sure, there is the M&M Act to argue with your dealer about, but i doubt that you will be successful unless you have a really cool dealership. For example, if your CV boots burst and you have a lift, then you are up the creek without a paddle 99% of the time. If your engine/tranny fails, then the dealership probably can't pin that on you and you would be safe.
Whatever you modify on your 4runner will void the warranty in that area unless it is connected to another area.