Question #2: When should I separate him out of the tank into his own safe place where the fry don't get munched by anything else in the tank.

ASAP. The longer they are in the display, the more likely they will be preyed upon by both things living (other fish, corals etc.) and non-living (the dreaded Maxijet Monster).

Remember to NEVER expose them to air. Use a large diameter siphon and let gravity help you bring them into a 5 gallon bucket (have more water mixed and ready for your display). You can also use a turkey baster with the end cut off (to create a larger opening) but I've had no luck with that or simply scooping them with a specimen cup.

Using a net or other means that exposes the fry to air is sure to kill them. Their swim bladders will overinflate (you can actually see a little bubble in their throat area) and they will die a slow death.