Unfortunately I doubt very much if there's a nitrogen deficiency. It sounds to me like it may have been drowned by a) not simply using a mixture (not layers which can actually defeat the purpose of quick drainage) of mostly grit - peat's terrible for holding water at the roots rather than draining immediately as it should, b) not simply planting the tree a 'few' inches from the bottom and sides, c) repotting too late in the season, d) growing it indoors(?) if you are, and e) just plain giving it too much water all around for the circumstances. You'd have been much better off to just plant it straight into the ground (it's hardy all year in your zone) and leave it for a couple of years.

It sounds to me like you got this technique straight out of a book and followed it to the "t". I did this too once upon a time. What else is one supposed to do? However, this information seems to be quite strict. Bonsai is supposed to be fun. Use your instincts.
The exact composition of the soil (in my opinion) is not as important as its ability to drain rapidly, if not immediately. Don't put any component into the soil that will pass through a window screen.
Declorinated water in a cheesecloth bucket overnight is not as important as making sure your tree is watered diligently, but only when the soil is just drying out. Directly from a dirty garden hose (with a rose sprayer on the end) if that's all you have.
Also, this tree has just undergone major stress, don't stress it more by pruning it.
I agree with Lucy, you missed a step that was a clencher here...Don't repot in late summer unless it is necessary.

Good luck with your tree, and don't give up. I have killed many trees that I loved, but there will be others, and I now know what not to do....sometimes.

Terry

That juniper is getting too wet. Junipers are a very tough plant. I have tortured many of them all different species. Remove that tree from the pot you have it in at this time. Inspect the roots, if there is any dead root (skin peels off easly, or breaks easly) cut it off where the live root stops. If you can put some fungucide on the cut areas. Repot the tree but this time use a quicker draining soil. Put your rock at the bottom of the pot. Then mix some potting soil (scotts or miricle grow tree and shrub blend) with sand, not silica just normal play sand. Mix the soil and sand at 40% sand and 60% soil. This should allow the water to drain quickly. Remember junipers can handle dry periods give it one every once and a while it is good for the tree.

IBG, rock should not go at the bottom - it's been proven to cause drainage problems rather than help them (which is why I advised about no layers before), and potting soil is terrible for junipers - holds water way too long, and sand is not a good idea either - larger grit is needed.