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Should I add parts to a Harley bike before breaking it in?

I am buying a brand new Harley Cross Bones. I want to do some performance upgrades to it such as an intake, exhaust and a Thundermax ECM with autotune. Is it alright to have the dealership add these parts before I actually take delivery and put the first 1000 breakin miles?

Should I add parts to a Harley bike before breaking it in?