This isn't an easy one to explain in a textural format.

You need to be "really" careful here. You can't arbitrarily just stop the model because you'll ingore the influence of the components (modeled versus not modeled) on each other.

If you're approximating things with a "static seismic" analysis then maybe you can stop the model (after extending it into the area of "no interest" and crossing three restraints). However, if you're performing a dynamic analysis I would not recommend you stop the model. If you do, your natural frequencies will be (very) inaccurate and your results (very) suspect.