The Sweepstakes race car that gets used at Old Car Festival is a complete replica. Two (maybe just one, I don't remember now) were made in about 2001-2003. Ironically, the "original" Sweepstakes car that is in the Museum is not original either. When Henry Ford was assembling the Museum in the late 1920s, he wanted all of his original, early cars to be on display. The original Sweepstakes did not exist, so he had a team of engineers make a copy of this famous race car in the mid to late 1920s. Some of the other cars Henry experimented with in between the Quadracycle and the first Model As of 1903 were built as well. The Sweepstakes car has been represented as an original at times over the years, but it really isn't-it is a 90 year old replica!!! There has been some speculation that there are some original parts on this car, but I don't believe so. The most current replicas are works of art and are fully functional like the original.
The 999 Racecar in the Museum is indeed the original. There have been some changes made to it. The car was raced and used for a few years after Henry was done with it, so it is not entirely identical to its original configuration, but, generally pretty close. Like all race cars, it was modified every time it was used. After it was retired from racing, it was on display at Billy Hughson's Ford dealership in California. Hughson was one of Henry's first Ford dealers in 1903 and was actually "collecting" cars while the Model T was still in its infancy. Hughson gave the car back to Henry when the Museum was being opened in the late 1920s. If you look real closely on the wooden frame rails, you can faintly see Hughson's name stenciled on the side.
George De Angelis wrote a very detailed description of 999 describing its history in an old issue of the Antique Automobile magazine, the national publication of the Antique Automobile Club of America. If you can get your hands on this article, it is a fascinating read. George was probably the foremost authority on this car.