compiler

In my MK mugen the statedef that correspond to the guard system are from 120 to 155 in the common.def.
In my case, if I wanted to do what you say, I should go to statedef 130 and:

; STAND GUARD (guarding)
[Statedef 130]
type = S >>>>> change to C
physics = S >>>>> change to C
ctrl = 0
anim = 130

disable this:
[State 130]
type = ChangeState >>>>>>> null
trigger1 = command = "holddown"
trigger1 =! inguarddist
value = 120

THEN, IN STATEDEF 152 :

change the animation:
; CROUCH GUARD HIT (shaking)
[Statedef 152]
type = C
movetype = H
physics = C
velset = 0.0
anim = 151 >>>>>>>>>>>> 150 (stand guard anim)
ctrl = 0

and finally change the value to statedef 130
[State 152, 3]
type = ChangeState
trigger1 = time = 15
value = 131 >>>>>>>>>>> 130 (stand guard statedef)

I hope this helps you or gives you an idea.

Do you just want both files to have the same name you choose?
If I understand your question correctly, happens that inside the .def file
the path and name of the .sff file must be changed to match it too

Look for this parameter inside the .def file: EXAMPLE

[BGdef]
spr=stages/STAGE NAME.sff

The answer is simple: in the data folder find select.def. From there you can make all the changes you mentioned, except add portraits in the selection screen (to do that you have to use the mugen character maker (you find it in the tools folder), open sistem.sff and extract with this software the image. pcx corresponding to the selection screen and add the portrait with any software to edit images (irfanview, xnview or photoshop) .then save the image again in sistem.sff.