Motorcycle Repair: Throttle cables, stock cv carb, stock cables

Question
Mike, I recently bought a S&S Super E for 03' Softail. I had a stock CV carb before hand. The problem I am having now is the current throttle cable housings are a little short while the actual cable inside the housing is too long. Do I need new cables for the S&S? Is there a difference?
Thanks for any help you can give me!
P.S. The current cables are not stock since I switched to ape hangers, however, I did still have the stock carb when I ordered those cables.

Answer
S&S cam out with housing for the cables which will work with the stock cables, so you didnt have to change cables. Are you sure your putting the right cable in the right place on the carb? Did you loosen the cable adusters all the way before trying to install?
Mike