Thanks for the pics. I can see how it all came together for you. A few comments - some mentioned already...
1) You can take the seedling out of the rapid rooter and put it right into the cloner after the tap root shows. By removing the rooter from your main aeroponic unit, it will reduce very small particulate matter from the plug clogging your sprayers. It will also improve the coloring of your roots - which is probably freaking you out a wee bit.
Stinkbud recommends rapid rooter for germinating - but not for insertion in his own bubble cloner (as I'm sure you know).
2) And yes - your bubbler was letting in too much light. Hope it's all better for you now.
3) I love the new cab and plan to do much the same with mine as you have with yours...except for one aspect of the layout. I got to tell you man, some of the stuff you have done here is very inspiring and it was a pleasure to see it all come together over the two threads. Really - I read both threads start to finish and was grinning and smiling the whole time.
Except for one part... where I wasn't smiling.
[soapbox]
I would really rethink the cloner bubblers and most importantly - the electrical lights sitting under your main aeroponic unit. Think about it cruzer - you have a rubbermaid container with two jury rigged drains being fed by sprinklers emanating from unglued 1/2 " pvc pipe, with rapid rooter plugs still in the system and potentially causing one or more clogs all at once at some vague and uncertain time...
And all of this is sitting 1/8 of an inch over sheet metal to which electric lights have been affixed. You have put electricity below water - and I mean - >>directly below<< it. That's the cardinal sin of hydro cab design. It's really not a good idea man. If your system springs a leak, or even if you just make a careless accident when adjusting LST, your goose could be cooked right there. Worse, you may discover the leak just as you touch the handle - or when you step in the electrified water seeping into the carpet. Either scenario (and lots of others you could think up) could fry your ass into a one way personal mission that will confirm or deny the existence of an afterlife. But one thing is for sure: you won't get the glory of posting about your findings
...or burn/injure you so badly you need emergency medical attention when you are in no state to clean up your house should the cops show up with the paramedics...
These risks may be very small - but whatever the case, it ain't worth it man. Rethink your layout and be safe!
[/soapbox]
And yes - I'm watching this one to the end. Thanks again for tending to the pics.