I think it is best to leave the roots undisturbed. That you can feel roots spread through the soil is a good thing. Your NIP's growth rate is likely to slow down now that it is in reduced light and that means its root growth will also slow down.
If you try to separate the individual plants, you will likely damage some of the roots. It is okay to leave the smaller plants in the pot, but if you don't the way it looks, then you can cut them off at the soil line, but leave the roots alone.
Cutting off the growing tip may cause that stem to slowly die, but there is nothing you can do about it.
Very bright overhead fluorescent lights may help some, but your NIP will need as much natural light as you can provide.
