You have what looks to be a myraid of issues, one *appears* to be a Calcium and Magnesium deficiency. You need to get a pH tester. These can be bought at your local grow shop or online for ~$7.
Leaving the water out for 24+ hours will allow chlorine to evaporate, and bubbling it will oxygenate it, but neither will pH it properly. For that, you literally need to test, then pH down or pH up as necessary.
Vinegar works for down, and baking soda works for up if you're short on budget.
-spek
ps. if you are using tap water, I would put an educated guess that you're too high on pH. If you can't get a meter, put about 4 drops of vinegar in 1L (~1 quart) of water, and it should bring it down to acceptable levels. Understand this is a HUGE guess though, considering I have no clue what your tap water quality is like. However, most claim they are around or just over 7, and you want to be ~6.4 for soil. Apple Cider vinegar works best.