My calamondin has 3 fruits and the 4th flower is open. My only concern is the yellowing of the leaves as seen in the link below. Any thoughts?

http://home-and-garden.webshots.com/album/573197100POkedp

I will further add that the entire container is filled with coconut husk chips. I have not fed the plant in quite some time (i suppose nutrient deficiency could be my culprit). Please don't yell at me.

With using an excellent draining medium with high aeration, your half way there, now start feeding your tree with a fertilizer that contains trace minerals, and your tree will reward you with a nice crop of fruit. Normally, the first deficiency symptoms that begin to show up, when a tree is not given the nutrition that it needs, is the lack of nitrogen (on older leaves, yellow leaves, or yellow-orange veins with some green on the sides. Note: that all new leaves are always lighter green for the first month or so until the tree has allocated enough nitrogen to them to fill in their green color. Lastly, looking at the leaves in the second picture, is the nitrogen source in your fertilizer derived from urea, and or is your water supply high in soluble salts? The yellow tips look like biuret toxicity, and the dead margin could also be from soluble salt toxicity. All in all you tree does not look all the bad. Take care. - Millet (1,305-)

Could be also, that some clacium and magnesium ist lacking, because the 'bumply' leafs may occur if the tree gets's not enough calcium and magnesium, so espacially if the soil/subtratum has a very low pH reaction, which reduces uptake of both essential minerals very strongly.

So take care, add maybe a little lime to the compost.