As far as " stock " goes under NHRA definition just as { pro stock cars) the bodies and engines have to be "stock appearing" . The term "stock " is used very loosly.
For many years Suzi's and Kawi's dominated NHRA Prostock bike catagory. Then when H/D came in with the sponsor $$$$$$ NHRA allowed the version of their road racing VR1000 engine. This is a fuel injected engine ,meanwhile the suzis and kawis had to still use carburated engines. Until I think 2 or 3 years ago NHRA let the Japanese bikes use fuel injection and in just a couple of years the suzis have caught up to the H/D and Buells and a SUZUKI now holds the e.t. record and i think the speed record also.
Turbos and superchargers a not allowed in prostock. The frames are custom built tube frames and resemble nothing like the street version.