Clones getting worse - Brown Patches and Purple Stems - Help please

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I recently purchased Obama Kush Clones they were 21 days old when I got them. I have had them for about one wee now. So they are not at about 30 days. This is my second attempt at a grow my first time ended badly with bad clones and bugs.

They have brown patches. Also the clones stems are starting to turn purple. The top of the plant stems are green the purple seems to be coming from the bottom and making its way up the plant.
What can be causing this?

I received comments scything this is a phosphorus deficiency and from my research online the pictures look very similar to those I found online.
I did a water change yesterday and put all new water and nutes into the system keeping the PH in range.

However this morning this plants look much worse. The pictures are from last night the plants have the same issue all over now and darker.
Do I need to add more of the FloraBloom? Would this help with the phosphorus deficiency? If so how much would I add to the system.


MY System:
Nutrients: General Hydroponics - Using their chart at week 3. Which is 10ml/gal of Miro 10ml/gal of Gro and 5ml/Gal if Bloom
Buckets: 4- 5 gallon with a control
Water level: about 2 inches below net pot system running 13 gallons total
PH: PH has ranged from 5.5-6.0 it has gone up progressively since I got the plants on 9/11/14.
PPM: 1000-1220.
Water Temp: 68.......it was 77 but just added a water chiller a few days ago.
Water Chiller: 1/10
Tent: 4ft x 4 ft
Inside Tent Temp: 73-77
Humidity: 50-56
Humidifier: 3 gallon cool mist
Light: MH 600 watt 18/6
Ventilation: 450 CFM inline fan to cool light
AC: 5000 btu running directly into top of ten
Fans: one 16 inch oscillating fan as well as a 6 inch fan by the ac hose
Airpump: 35 watt with 2 inch air stones in each bucket
Water pumps: Main pump is 950 gph that controls the system and one 185 gph pump running to water chiller.

 
Your PPM is high, and you must keep your PH in check. You will need a PH pen and corrective solution. I would bet that PH is the cause of your deficiency. What I see is nute burn, and slight stress (probably PH related)
 
All your chemistry seems dialed in.

Two possible things come to mind:
1. you have root rot (despite your chillers, etc) and need Dutch Master Zone or EZ-Clone's CLear Rez.
2. Your air circulation is too aggressive. I have had plants next to too much air flow burn like that while those further away, receiving a gentle breeze, would be doing great.

I suspect it's one of these two things. You can add 1 drop of bleach per gallon as an alternative to DM Zone or Clear Rez, it wont hurt. Also, the chlorine dissipates quickly, so after you add it, re-add ever 3 days. remember, the bacteria or fungus could be on your ph/ec meters, so add the chlorine AFTER you check all your numbers and adjust pH/ppm/EC.

keep us posted, we're all learning here.