Just wanted to second this post. In my experience any sort of deficiency and/or toxicity is typically related to problems with your soil and/or your watering practices/schedule. Most problems we will experience with organics has more to do with your soil being properly balanced as opposed to having too little/too much of something.
If you over-water your soil it will cause all sorts of issues that look like deficiencies. Too much water in your medium can throw off your pH over time because the constant supply of water will be reacting with the nutrients/elements within your soil medium, as a result you'll start seeing false "deficiencies" or "toxicities" that is usually your pH being out of whack 9/10 times.
The idea of organics regulating the pH itself is often misunderstood and is the reason why many people believe they do in fact have deficiencies/toxicities. Yes, a living organic soil is definitely able to regulate it's own pH, but only when the soil itself is properly balanced. A properly balanced soil doesn't just have to do with the types of amendments that are in it, but also the quality of the compost/EWC in the mix, the amount of aeration/oxygen in your soil, and the amount of water as well.
Too much water will make your medium's pH out of whack, depending on what the water was reacting with in your soil at the time will make your pH either too acidic or too alkaline. Either way this is a problem because if your pH isn't in the 6.5-6.8 range you will experience lock outs that will manifest themselves in the form of "deficiencies". Like your nitrogen problem for instance; you had a clone in the soil for 3 weeks, I highly doubt that a 6-12in clone used up all of the nitrogen in the soil. The only way you could actually be out of nitrogen in your soil is if you used something like blood meal and/or guano in the soil and let things go anaerobic when you let it cook. If your soil goes anaerobic, that nasty smell it gives off is actually ammonium gas and that smell is literally your nitrogen evaporating from the soil. This could also be an issue even with a plant in the medium, as if your soil has too much water then there isn't enough oxygen and therefore only anaerobic microbes can survive, meaning your nitrogen is all being lost in the form of ammonium gas. If you haven't smelled any ammonium, this likely isn't your issue, and you would know if you smelled it believe me!
So, if you still have nitrogen in your soil, but your plant isn't getting any of it then the only explanation here is that you're actually experiencing a lock out due to too much water and/or too little drainage. If I may recommend, get yourself a moisture tester and a Chapin sprayer as that will allow you to water as optimally as possible aside from maybe Blumats or something. Unless the plant is completely rootbound I NEVER water until I see runoff. Only water like that when you know you have a rootbound plant, otherwise there will likely be way too much water in your soil with such a tiny clone. Remember, the roots are what uptake the water in the soil, so if you only have 1g of rootmass and 5 gallons of soil you only need to provide enough water for the microbes to survive and for your roots to uptake. With that in mind, the amount of water you give will be directly proportional to the size of your root mass. I've been growing on and off for nearly 7 years, the last 2-3 years have been living organic soil. I've only just now started to realize just how important properly watering is because I've been messing it up for that long. Most of the problems I've ever had as well as many of the problems I see people on here have are almost always related to watering.
If I may, allow me to ask a few questions? I'll be able to help much better when I have an idea of what your exact situation is instead of continuing to type out a miniature novel xD
1) You said you just transplanted the 1g to a 5g pot. How often have you been watering the 5g pot and how much water do you give your clone when you do water?
2) You said your 5g pot has amended soil in it, could you tell me more about what is in your soil exactly? How long did you let it sit and "cook" for? What, if anything, was used to inoculate the soil?
3) What ratios are in your soil in terms of peat/aeration/compost? 33% of each? 50% peat, 30% aeration, and 20% compost? What ratios did you use?
Get back to me with the answers to those questions and I'll do my best to help you out.
For what it's worth, unless you're in flower you shouldn't be too concerned about stunting. When you're in veg, the worst case scenario with mistakes is that you have to veg for longer than normal so they can recover.. but they are more than capable of recovering from just about anything in veg. My air conditioning went out for 6+ hours one time before I noticed, my girls were in 122 degree heat in a sealed room with zero air conditioning or ventilation. Fortunately I was running CO2 and supplement with silica, otherwise they likely would have died for sure. 6 hours in 122 degree heat and they weren't even droopy. I did experience mediocre yields with that grow, but it was due to errors I made in flower, not the heat stress from veg. When you're in veg, unless the plant is 100% dead you can bring it back with enough time and care. Hopefully you're in veg as that will allow us to take our time with this issue and allow you to properly troubleshoot not just this issue, but hopefully provide you with enough information that will allow you to have a seamless grow come flower. Come flower, there are no second chances unfortunately..