We recently found out that the 03 and up TW's have a slightly different exhaust mount than the 87-02 TW's. It's only off by about 3/4 inch. Your aftermarket mufflers might be made for the newer bikes. You can probably fabricate a flat bracket. If you need any advice, post some pics with the back part mounted, and somebody can probably help you.
Check out this post for more info: