Hey man. Just wanted to let you know you didnt do bad for your first time with the producer. Here are some tips that i have learned using this box and doing Bubbleponics.
1. Less is more. Use less ppm's for younger unrooted clones and/or seeds.
2. GET A WATER CHILLER!! I suggest a 1/10 HP and NOT chiller ICE probes.
3. As you might know by now, genetics mean everything when you have limited space. Choose your strains wisely and watch out for large colas and bud rot.
4. Stake your plants. Net trellis, chicken wire on a frame or small diameter wooden dowel rods work great.
5. Your PPM's on your CO2 should follow the PPM's in your res. You can even run it lower than that.
6. You should replace the intake and exhaust fans on your unit with small blowers. It makes all the world of difference when it comes to keeping your unit running cooler.
7. Watch the stretching. Too much time under that CFL and those babies get lanky. I understand you had some rooting problems, but I think your on the right track with the extra airstones.
Overall I think you did pretty well for your first time using this thing. Keep it going and i look forward to any of your next journals. Peace.