Mortal Kombat 3 has some known issues to name a few:

-the problem with the speed of the menu.
-Problems with small freezes and some problems with the control drift

Also, rescaling it is somewhat complicated.

But I think I have found the best way to configure it, and I am going to show you, in the “dosboxMortalKombat3” file, located in the game folder, we modify the following:

fullscreen=true
fulldouble=false
fullresolution=1920x1080 #(or your resolution)
windowresolution=1920x1080 #(or your resolution)
output=ddraw
autolock=true
sensitivity=100
waitonerror=false
priority=normal,normal
mapperfile=mapper.txt
usescancodes=true


[render]
frameskip=0
aspect=true
scaler=rgb2x

[cpu]
core=auto
cputype=386
cycles=53000 #above 60000 cycles the control experiences drift
cycleup=1000
cycledown=1000

#This largely resolves the freezes and also improves the fluidity of the game, It also improves the fluency of the inputs.

[joystick]
joysticktype=fcs #The "fcs" parameter is the best option in both cases.
timed=true
autofire=false
swap34=false
buttonwrap=false

#For the xbox control to work we must close steam or things like joytokey, if we already configured the mapper we must delete the mapper.txt in the game folder. The only problem is that the block is done with a low fist and a high fist pressing simultaneously. To run, it is with high kick and low kick simultaneously. This does not allow d'pad, joystick only.

*Another way to configure the control is with mapper which is with Ctrl+F1 when we open the game, then we click, for example, on the letter W then we press Add with the mouse and then Up with the Dpad of the controller, The advantage of this is that we can assign unique buttons to run and block.

#The "fcs" parameter is the best option in both cases.

and that's it.

PD: I speak Spanish natively, so I hope it is not difficult to understand and if someone needs it in Spanish I will gladly help