Which trans front plate ar you running, GM or ford/viper/retro? Is your slave an internal or external? How much 'shim' is under the slave (if internal)?
If the volume of the master is to large, maybe a Viper slave would work (if front plate is the ford/viper/retro one). I have a Viper slave, SC master, single disc clutch in an older BW LS1 T56 with viper/retro front plate and about a 0.4" spacer disck under the slave.
If you have shim, taking it out will move the stroke complete point lower to the floor, as long as the slave is not over-extended it should be fine. The slave will only retract as far as the point where the pressure from the pressure plate via throwout bearing= slave/throwout spring pressure.
Finding a slave and master that will work together and give the preferred pedal height for dis/engagement would be my pref. Using a stop on so short of pedal movement ...not so much. If you moved the pedal pivot or master pivot to reduce the moment felt by the master would probably work(more pedal travel with less master push rod travel).
MikeH