Nice set of pictures!
The tender top leaves look seriously deficient in Zinc and Copper, and the previous flush looks mildly deficient in Iron--- so the new growth is probably also deficient in Iron.
Spraying the Southern Ag Citrus micronutrient mix at a dilute / weak / lowest-recommended rate, with some kelp added, on the new growth and on the still-hardening-up previous flush, in the very early morning, or before sunset, would be more effective than the drenching in this case--- as you have already found that not enough is rising from the soil, to some portions of your tree.
As Ibliz pointed out, the scorch marks do look like thrips damage--- but that still needs to be verified.
Do you have a traditional magnifier, in the 8X to 16X range? Or a digital camara phone attachment to take microscopic pictures?
The stem blackening looks like anthracnose.