'08 and up Buell ECM's are all DDFI-3 regardless of model. If it runs well with the 1250 kit on it I'd leave the tuning alone. The website the Buelltooth came from has much info about tuning, but 1250 tunes are harder to come by. If you can't help yourself and have to mess with it, be sure to save your stock one.
Get whatever exhaust you want, but know the bike was probably tuned for the one thats on it. Although most aftermarket exhaust tunes are nearly identical they are usually for a stock (1203) engine.