My first thought for the yellowing leaves is a nutrient deficiency. Looking at the pictures on this page
http://lemoncitrustree.com/store/pest-disease it seems to most closely match an iron or zinc shortage. (the bottom two images)
The brown spots made me think immediately of spider mites, but it also closely resembles one of the fungal diseases on this same page.
If I were dealing with this tree I would first give it a good dose of an organic fertilizer (a thick layer of
compost might suffice).
If only a few leaves are affected by the spotting, I would remove them before the issue could spread. (this would be the same whether insects or fungus) If you have any good local nurseries, bring a sample of the leaves for the employees to look at. They should be familiar with the common ailments in your area. Even if they don't offer an organic solution, just knowing for sure what you are dealing with can make it easier to do more complete research.
Often just improving the nutrition of a plant will give it the fortitude to fight of diseases or pests on it's own. Citrus are one of those plants that can recover from extreme defoliation.