First grow

[tevfik]

Is there anything I can do to ensure this is not his demise?

Just relax. She/he will be ok.

The roots were all around the basin of the cup, some were even sticking through the perforations
I should have planted them higher in the pots though. I will probably just be keeping whichever of these are best, as mother plants. If not they will need one more transplanting into bigger pots.

There are some reasons for that. One is soil stays dry on top and wet on bottom, all the roots go there. This is very common in this size of pots. Since you have bigger pots you shouldn't water often. And make sure the soil is equally humid.

Yes you should planted higher. You don't need that much empty spaces on top. Just 2 cm is enough. I even go with 1 cm. Higher is better. They roots go deeper, so you need more height in soil.

Its too early to decide about mother plants since you have many. When i grow like this first big plants were always turned to male.
For flowering yes you'll need one more transplant. This is exactly what i do. First i germinate them in small pots then transfer to bigs like yours. After sexing i am transplanting in to final size and switching the light schedule.

In the end you're ok. Keep going :thumbsup: