Alot of aftermarket stuff has more "meat"(mass) in them than stock, and so clearances can sometimes be an issue(especially known for lowering spindles). Is it hitting somewhere that would allow you to mill(grind) some of the metal away without losing stability or strength? I wouldn't cut anything on the upper control arm unless you were going to notch and brace it, and then I'd be more comfortable in getting a tube upper arm over cutting the stock one. Try comparing it to the stock spindle and that should give you an idea of what can be removed, just don't remove too much at once, little by little, can always take more off, but never add more on...without welding, and welding cast is tricky.
