what time units does this simulation stop time use? is it seconds or msec? or is there any method to measure this time as some time I feel 1 unit of this time is not of constant length?
It's seconds. But Simulink does not run in real-time, so one second of simulation time can a lot less than a second of real-time (if your model runs very fast) or a lot more (if your model runs very slow).
If your model runs "too fast", you can use utilities such as Simulink Block for Real Time Execution, Simulink® Real Time Execution, Real-Time Blockset 7.1 for Simulink, Real-Time Pacer for Simulink or RTsync Blockset (there are plenty to choose from) to slow it down to real-time.