Show some pics of the clones I may be able to help
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Thank you! Here is the history on the clones. I didnt want to clutter up this thread. You can reply in either place is fine with me.
Here is the short version: Bought 5 clones of Blue Dream - 6"-8" tall. They looked pretty good but had some droopy leaves. I was paranoid about bringing in bugs, so I completely dunked them in a waaaaay too strong batch of neem oil and nearly killed them all. After rinsing a couple of times, they started to come back and are sloooooowly recovering. They are in small rock wool cubes and all were showing some degree of nice white roots in the beginning. 6 days ago I put them into dixie cups of perlite with small holes near the bottom of the cups and have been bottom feeding them with 6.0-6.1 PH water and low dose nutes. Lights are at 20 watts/sq ft. Ive been removing the dead leaves every so often if they were dry and crumbly or totaly yellow/white and easily plucked off. The new growth looks ok but its going slooooow.
However, after 6 days I only see one single small new root on one plant showing in the cups. Id like to pick the best three and start them in the hydro totes, but if its going to take weeks and weeks just to grow roots that wont work.
Here is what they looked like when I first got them.
A few hours after the neem dunk
Today:
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They’ll bounce back within a week or so would be my guess, just wait for them to de shock and start new green growth again
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Ah ha! I am willing to bet you are a charter member of the LITFA club! 
I was afraid you would say that, but I think you are right.
These stupid things are bound and determined to mess with me. I just checked them over and that one small root has doubled in length since this morning! Plus, there are some more small ones showing on the top of that cube.
Ok, I guess I will wait some more. Im not very good at LITFA 
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What’s litfa? 
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It stands for Leave It The F Alone.
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Sorry! I thought everyone (but me) was in on that weed joke
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I agree with @h3y4rnold. You smothered them with neem. (Bugs also)
Thing is, one neem treatment is not enough.
You have a choice,
fast growing out the door,
or no bugs.
Now you have me worried again. Are you saying I need to treat them again with the neem?
Its been 10 days since I did the neem drowning thing and no sign of bugs so far. I was hoping that if no bugs showed up after two weeks (4 more days), I would be good to go. Remember, there never has been any sign of actual bugs. I did the treatment out of an abundance of fear, but there was never any evidence of live bugs.
If I do treat again - exactly how should I do that? What strength of neem oil should I use and should I dunk or just spray the leaves? Should I dunk the dixie cups to flood the root zone? For how long?
Im very wary of doing this again. I would prefer to just wait a few more days rather than treat and risk another 10 day delay.
By the way - a second plant has started to show roots and the first one has a second root showing and it is growing fast, so they are recovering.
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This PH issue has been persisting. Overnight my PH in the rez will go from 5.8 to 6.4. Thats in less than 8 hours and with NO plants. Just water and nutes.
So…I decided to repeat my tests on everything but starting with the water PH’ed down to 5.11 at the start instead of the normal 7+ that my tap water is at. When I did the tests the first time, I just used tap water without PHing it down first and I saw no changes in PH when adding lava rock or perlite that time, but I decided I should check to see what happens when starting at a lower PH.
First, I checked the calibration on my meter and it was just fine - as it always is. I re-calibrated it anyway as long as I had the reference solutions out anyway.
Then I split the PH’ed water between several jars and put some lava rock in one jar, some perlite in another jar and some nutes in a third jar. I kept one jar with just the ph’ed water only.
Im using General Hydro’s PH down for this test - not vinegar.
Its been about 9 hours since I started the test.
The PH’ed water went from 5.11 to 5.18 = + .07
The PH’ed water plus lava rock went from 5.38 to 5.84 = + .46
The PH’ed water plus Perlite went from 5.34 to 5.71 = + .37
The PH’ed water plus nutes went from 4.93 to 4.97 = + .04
So - every darn thing in my system is raising my PH!. Actually, the tap water and nute water changes are pretty small and could just be meter errors, but the perlite, and especially the lava rock, are definitely buffering my PH up.
Im not sure what to do about this. I cant afford to buy new stuff and start over, plus there is no guarantee that the new stuff will be any better.
The only thing I can think to do is try to neutralize what ever is in the perlite and lava rock thats causing the buffering. To do that I have added 3/4 of a gallon of vinegar, plus a 1/4 cup of PH down to the rez. Its at a PH of 3.3 at the moment ,and Im going to let that circulate for a day or two.
Anyone have any other ideas?
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Perhaps your tap water is the issue. Try the experiment again using distilled water and let’s see if the issue is still there. I assume you rinsed the lava rock and perlite to get rid of the fine dust. Where did you source the lava rock?
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Yes, the lava rock and perlite were both rinsed very well - in my tap water. The lava rock was from Home Depot. The perlite came from a local grow shop. I just checked and the perlite bag has absolutely nothing written on it, so no clue who made it or where it came from.
Also, I just noticed some of the perlite does not float?
I think you’re right about the tap water being at least part of the problem. This morning bth the ph’ed tap and the nute water have both gone up significantly, but the lava rock and perlite have gone up even more.
After another 10 hours of soaking, the readings this morning are as follows.
PH’ed Tap water alone has gone from 5.11 - 5.18 - 5.46 = + .35
Tap plus lava rock has gone from 5.38 - 5.84 - 6.25 = + .87
Tap plus perlite has gone from 5.34 - 5.71 - 6.10 = + .76
Tap plus nutes has gone from 4.93 - 4.97 - 5.62 = + .69
I guess Im going to have to see about buying some RO water or put this project off until I can afford to install an RO system at home.
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When I was using tap water direct into my system, it would mean I constantly had to add PH down to keep the PH where I wanted, even with roots lowering PH when feeding. I found that, like you, I had a constantly rising PH no matter what I did.
Then I got an RO system and I find that my PH will wander up and down, with no particular direction until the plants start to feed heavily at which point it will constantly lower, meaning I have to add PH up to get the PH I want. This normally happens by about week 2 of flower. Until that point, if I want a particular PH I need to add PH up AND PH down to buffer the solution and allow it to be stable.
It is because of issues like this that I now use an automated dosing system. it looks at your nute levels, and PH and if they go out of range, adjusts them to be in range. It does this every 10 minutes, even while you sleep. When I refill my system I just turn on the valve to the RO system, it starts adding RO water to the tank, when the level is high enough I start the pumps and the doser which then puts nute levels and PH within range before the tank is full and keeps both within range as it fills and from then on. When the tank EC and PH are within range I add plants.
As such, I can leave my plants for weeks at a time, as long as I can see my graphs I know what they are doing.
In tap water there are usually high levels of calcium etc which will buffer the water to a high PH meaning to maintain a set, lower, PH you need to constantly add PH down. As water is taken up or evaporates, more high PH water is added meaning that, again, you have to add PH down. This is fairly simple, although frustrating.
If you get an RO system, you will find you need to be even more vigilant on your PH as it will vary in two directions instead of only one. It will even possibly vary more as the water is unbuffered.
It seems that your lava rock, your perlite, your tap water AND your nutes all raise PH. All that getting RO will achieve is meaning your lava rock, your perlite and your nutes are raising PH.
Personally, I would fit a float valve running to a tank filled with water slightly more acidic than you require, then when your plants take up water, or water evaporates, the replacement water will slightly compensate for the raising PH.
Getting RO will make your system more volatile, which means more growth if you have everything dialled in, more headaches if you have not.
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well crap - plus extra letters for no good reason…
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@MicroDoser gave you a good answer.
the alkalinity of your water and what it contains is the problem. What are your ppms from the tap?
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Most of the time its around 120-150 PPM, but Ive sen as hi as 220. Conductivity is around 120-180-uS most of the time and PH varies from 6.8 recently up to 7.8 at times. Mostly its around 7.1-7.4.
Im on a community well that serves maybe 30-40 homes in the area. Maybe its being treated some how is why the variations or maybe thats just due to how ever much rain we get - which is a lot. There is no smell of chlorine or fluoride treatments, so if they are treating it, I dont know with what. I considered calling the company that manages the well and pumping house, but I decided it wouldnt make any difference. They are not going to change what ever they are doing, so Im stuck treating this water or going RO no matter what they say.
Im out of time and money, so its either toss out the clones, drain and clean the system, and try something different next fall after it cools down, or say screw it, and try to make this work anyway.
The worst that can happen is I kill the clones, and waste some time, nutes, electricity and what not.
Ive grown kind of attached to these clones after trying so hard to kill them. It wouldnt be right to toss them in the trash after they have worked so hard to survive.
I think I will say screw it, and just go ahead and try this anyway. Ive got two gallons of vinegar, and about 2 cup of PH Down left, so I think I will see how far that gets me. If I kill them in the end, at least we will have made a good fight of it
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Hmmmmm is there anything you can use in hydro to buffer the ph like you can in soil? Ive read of using pine needles and other odd things in soil to help hold the PH down, but never heard of anything but PH Down and similar acids, vinegar, battery acid, lemon juice etc to use in hydro.
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Whatever you do do not give up.
I managed for years with water at PH 8.1 350TDS.
Unfortunately, what it means is every time you deal with your ladies, you will be adding some PH down.
Later, when they start feeding strongly, they may adjust the PH by themselves.
If nothing else you will become a ninja PH downer 
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The best buffer is your nutrient solution. the more ppm’s the more it will buffer. The more the buffer the more acid it will take to move the ph. unfortunately, this doesn¡t help you with your current problem because you need low ppms now.
example, R.o water with 0 ppm with a hypothetical ph of 8 will require one drop of acid to lower the ph to 7
tap water with 300 ppms and a ph of 8 will require 10mls of acid to drop to 7.
the r.o with no buffer and a drop of acid will give you a very unstable ph reading. also it depends on the type and strength of the acid.
When I have ph problems and if possible i will mix my solution a day before using it. sometime the ph drift is slow. by doing it a day in advance the acid has time to do its thing and the swing should be done by then. (allways mix my clone water one day early)
Well water is another problem completely different. is it raining. rain can leaching the wrong kind of minerals into the well water. This is a common problem with using a well and growing. The rainy season always brings complications like dramatic ppm and ph swing from one day to the next.
so in short,
maybe if cost is a issue, try to get some concentrated acid. Any grow or agricultural store will have it.
nitric acid for veg
phosphoric acid for flower
a couple bucks for a litre and it will last for years. I would dilute it first before adding it. I make my own dilute so it is already prepared for when i need it.
AAA RULE FOR ACID
ALWAYS ADD ACID AAA ALWAYS ADD ACID
never add water to acid.
also, like @MicroDoser said. don’t give up. if anything try something radical to see what happens. I do it all the time.
actually what is the status now??
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Thanks guys!!!
The status now is I decided to drain and clean/flush the whole system and start over with fresh water. I spent several hours doing that yesterday, but now Im out of General Hydro PH Down. I decided to stick with that instead of vinegar as long as possible.
I’ll call some local hydro shops and see what they have for nitric/phosphoric acid.
These clones may not be vegging for long. They are mostly sativa and are supposed to grow tall - over 72". which is way too tall for my tent. I was planning to switch them to 12/12 almost immediately. Actually, I figured I would keep them vegging until the roots got well established or they started to get too tall - which ever cam first. Im going to scrog again, so that will help.
Thanks guys! You have both helped a ton!!!
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