If you had actually gone through the clear, the area where you have the black transfer to your rag would be much duller than the rest of the paint. It would be damn near impossible to go through the clear doing things by hand, you'd have to use a rotary buffer and even then you'd have to do something wrong to burn through.
www.paintscratch.com says that the Black Ebony on 99 Contours is a basecoat/clearcoat paint.
Silly question, but are you sure you just weren't near some of the black trim?