Well, sometimes it does works for some simple move like a KFM taunt.
But, for something more complicated like a Projectile (fireball in essence), I think you still need to modify Ryu's Hadouken MUGEN code to work for Dan's. At least you need to modify the collision boxes and frame timings and when and where the Hadouken takes place with respect to Dan himself.
And, neither Ryu's Hadouken MUGEN code nor Dan's Hadouken MUGEN code can fit your SNES MK2 Johnny Cage's Projectile (fireball) I guess........you still need to make your own or study other mugenzied MK2 Johnny Cage's MUGEN code...........
I remember your MUGEN SNES MK2 Johnny Cage WIP here: http://mugenmultiverse.fanbb.net/t5048-i-am-making-johnny-cage-mk-2-snes-version
Keep up with your MUGEN SNES MK2 Johnny Cage WIP!