by the way do you run your mister/sprayer 24/7 with the rapid rooters?
When I plant my seeds (every once and a while clones), I put them in the plugs then in a humidity dome. Once they are ready to come out of there the go into their net pots, now with neo tops, and there they live out the remainder of their days. You could leave them in the cloner you made and grow them in there (Though a min 2" pot for that). The only problem you will have is your chamber is also your res. So once the roots got long enough it would become a deep water culture.
As for timers I am going to repost one for before
First ask yourself what is the point of aeroponics?
To increase O2 to the root system. If your water is always on then your roots are always wet. If they are always wet then they are relying on the O in H2O. So basically put deep water culture (effective) BUT just because it provides results doesn't mean you cant do better. If you give your plants time to "dry/drink" they will take in the o2 from the air. then spray, they grab nutes and so on. Another VERY important factor is the temp of your water.the difference between 65deg water and 75deg water is 65 has upto 60% more o2 .