I consider a clone to be a car that tries to exactly duplicate an original. Same badges, clamps, markings, colors, etc... Not saying that everything has to be exact, but at least appear that way.
Custom, to me is when the owner tries to do things differently than the originial. Could be putting different options together that orginally would not be available together, modernization of the car, or just getting creative with body work and or paint.
This being the way I look at it, most old muscle cars fall in to the custom category for me.