Its all pure speculation since he never faced anyone near Cotto's calibre, but I think pre-prison Ayala stops Cotto. Too big, too strong, too much firepower.
I think you mean the pre-jail version. The rapes didn't take anything out of Ayala, rather his victims were the ones who came off 2nd best.
Margarito gave Cotto a much worse beating and was clearly a better fighter before he fought him. Ayala is a myth, I'll go with a real good fighter. Cotto UD.