Not too early. (for your predicament.) Just make sure current doesn't push the young away from the egg yolks once they pop outta them. They need to feed on the sacs for a couple days.
Once they become free swimming (and spreading themselves out) you can start feeding them fry food. I usually take an ugly-algae-covered rock from another tank and pop it in as an alternative food source as well.
I've had LESS success with this seperation method, but in your prediciment it seems like the only way. I think only small amount made it in mine though, cause they were seperated from their egg yolks as soon as they popped out and became wigglers. I would suggest no substrate.
Just curious, did the kids ever make it to wigglers before or were the eggs always eaten?