I believe you will find the mounting brackets to be off alignment since it's a different model.
I have read that the '99 and '00 are the same, and that supposedly in '01 they changed and would not fit the '99-'00...maybe someone else can verify this...maybe the exhaust port on the cylinder changed after '00, I don't know.
When I got my '00 in boxes/pieces...it had a '94 FMF fatty with it....I wasn't aware of this until it came time to install it after completely rebuilding it. The mounting brackets on the pipe were about 2" off from where the frame mounts were. The previous owner(15yo kid) had apparently had it strapped on by just the exhaust springs!, which explained why the eyelets for the springs on the cylinder were worn right through!.
Bottom line, you "could" modify it to fit providing the outlet on the cylinder isn't different and the stinger doesn't hit the shock body, then all you'd probably have to do is cut the mounting brackets off the pipe, and relocate and weld them back on so they line up with the frame mounts...but you'd be way better off to just find the correct pipe for your '03, and bolt it up and ride issue free.