I also have a 97 Supersport with an FCT. I purchased a 2001 SAN cover from someone and am using that. It fits ok and is good for keeping the rain out, etc., but there is no way I would tow with it. The fit isn't perfect and I would hate having it flopping around and scratching my gel coat. If I were you, I would get a rankin cover. I have heard these are the best you can get. They will send you a form to fill out giving them the dimensions of your boat and where the tower legs are located, etc. They fit super tight and are trailerable.
Check out www.planetnautique.com
. Do a search on there as a lot of them have the rankin. They actually had a group buy on these covers at one time.