I have a Meyer Lemon tree, its about 5.5 ft tall. Its dropping leaves like crazy. The leaves are falling close to the trunk first. Its lost about 80% of its leaves.

I checked the roots, they don't appear to have root rot.

I do live in michigan, it has a 200 watt hydrofarm cf light above it. I've also got a humidifier right next to the plant.

The leaf drop has slowed, but how many can fall before the tree dies? Should I prune off the branches with no leaves. Could this be a nutrient deficiency?

No, it is most likely because the root zone is too cold. Try using a heat mat & you should see a great improvement. Do a search on WLD (Winter leaf drop).

Welcome to the forum by the way.

It did improve greatly since I put one under it like 2 weeks ago. Its full of blossoms, should I cut them off? About how long does it usually take for it to turn around?

Anything else I can do to warm it up?

No, just get the roots warmed up & it will take care of itself. It will drop whatever fruit it can't support.

Do new leafs come out on existing branches or new branches? Should I prune branches without any leaves (they are all still green)?

No, it will re-flush just give it time.

What does re-flush mean?

Flush is the term used to describe the growing of new leaves. The new leaves will develop on the tree's present branches. - Millet (343 ABo-)

Meyer "lemon" is such an amazing tree, probably one of the best for beginners, your tree will come back with a vengeance this spring, I have no doubt about it. I have beat up my Meyer tree more then any other tree I have, its a wonder its still alive.

I'm just anxious because the leafs are falling. I think it will be okay, I'll focus my attention to figuring out how to prune my 2 theobroma cacao trees

What is the physiology of how they survive when the leaves are gone? Are they not starved for energy or do they have a surplus?

The simple answer is energy is stored in the twigs, branches, trunk and roots. This explains why a tree can completely defoliate and still survive.

To add to Ryan's post: When a tree drops all or most of its leaves, the tree is still capable of generating a little energy. This is because the trunk and branches contain chlorophyll (the green color of the wood). Whether the tree will flush new growth in the spring or not, all depends upon the amount of carbon that the tree has stored up. When a leafless tree once again flushes a new canopy of leaves, it uses up almost all off of the carbon (energy) that it had in storage. Therefore, it is very important to carefully care for the tree for the next couple months, so that it is able to regenerate more carbon (sugars) as a backup energy supply. If the tree should lose its leaves again shortly after recovering, either by poor care, insects, drought, or any number of reasons, it will surely not be able to recover, and will die, as it will have no back up energy to regenerate itself. - Millet (340-ABo-)

As far as I know the citrus trees unlike deciduous fruit trees they store the energy in the leaves, a very small amount in twigs and almost nothing in the roots.