I would tend to believe Shelby's claim as to the most cars. There have been 80+ companies making Lotus 7 replicas over the years, I don't know if the Cobra can beat that claim.
Kit Car Builder magazine has stated the same opinion as to total production. Factory Five gets several hundred of their Cobras at its annual event.
There are replicas of many sports cars. Ford GT-40, Lamborghini Countach, Jaguar C and D types, XK120/140, MG TD, TF, and an older model I can't remember, Porsche Speedster, 550 Spyder, 904, 917, 2 seat Thunderbirds, Ferraris of several types, Allard JX2, M-B 300SL and many more. Pick up the annual edition of Kit Car Builder magazine that has a listing of all the different current kit makers for a comprehensive list.