If you raised the front high enough that you needed to cut out the stop for the upper control arm, then your stock shocks are not long enough. If your shocks are maxxed out in length during normal suspension travel, maybe you are hearing that? Lift & level kits come with shock relocating brackets that allow using the stock length shocks. Also, many shock manufacturers offer shocks for lifted trucks, you could use shocks for a 2-3 inch lift. That would be a better choice if your shocks have some miles on them, or if your wheel/tire combo is larger or heavier than stock.