I'm sure I read somewhere that any mod that does not effect something your claiming for under warranty should be fine.. I.E... If you have lowering springs and one of your dampers (if your keeping the standard ones) gets shot it will not be fixable under warranty because the springs caused the damage, but if you have an issue with something like a faulty electric window its fine because that mod does not in anyway contribute to that issue.. If you get what I am saying haha..
As for pads/disc and tyres that's no issue what so ever, the rest would need declaring to your insurance also.
Hope this helps
Edit: Dam it! Beaten again! haha