my advise, start all over and use kfm.
After lookin at your cmd file, I agree with WanteD. Don't scrap the sff, but I think the cmd and possibly the cns need to go, most definitely. I'm gonna mess around with it for a few minutes here, but it looks as if you're gonna need to redo it
The main problem in the cmd is stuff like this
[State -1, Stand Light Punch]
type = ChangeState
value = 1triggerall = command = "x"
triggerall = command != "holddown"
trigger1 = statetype = S
trigger1 = ctrl
trigger2 = stateno = 200
trigger2 = time > 6
value = 1 is a big no-no. The standard value for a light punch is 200, and if memory serves, mugen wont recognize the move if its any other state. If you haven't already, read the Narutorials on Cyanides site to see what I mean.
EDIT: Another problem I found, I'll post as I find them
[State -1, Crouching Uppercut]
type = ChangeState
value = 4
triggerall = command = "b"
triggerall = command != "holddown"trigger1 = statetype = C
trigger1 = ctrl
Thats a major NO. You can't have a command to trigger a crouch move where you're not allowed to hold the down command. Plus, the proper state for a crouching light punch (I believe this is his light punch) is 400, so the value should equal 400 and the statedef in the cns for the crouch punch should be 400 as well.