Those surely were roof rats. I'd also be worried about where they are bedding down. Really sorry about your tree. Not sure about how to proceed and interested in hearing from some knowledgeable forum members.

The roof rats that ate your fruit are not to blame. Trees are living things and sometimes living things just die. The termites are a greater worry; we regularly treat all our Meyers with anti-termite chems, as a colony can eat the roots and kill the tree.
As for replacement, I would first treat the soil in the area for termites; I would pull the tree out getting as much of the root as possible; I might add a little amendment such as compost or new dirt; and I would plant a new Meyer in the same place. If you want a semi-dwarf, I would probably order my tree (the biggest and best you can find/afford) from Four Winds; if you want a full sized tree (up to 10-12 feet for a Meyer), I would order it from Citrus Tree Source on C-35 or Macrophylla root.
If you do that, you should have fruit again in a year or so and much more soon enough, if you fertilize and water prudently.

Thanks, John!

What type chemical is a good choice for killing the termites and not harming the tree/fruit? Is it something a private consumer like me would have access to?

I'm guessing we had a regular (non-dwarf) tree since we kept it pruned at about 7ft tall with branches growing up much higher in between prunes. Citrus Tree Source seems like a seller to commercial/large scale buyers- I just need a single tree,

I can't claim to know much about growing citrus in your part of the world, but it seems clear to me that the photo from 5/2014 showing the base of the trunk is the one to concentrate on. The bark is entirely missing at least half-way around the tree. If it's the same around the back, then that's the reason for the sudden death. All nutrients and water flow through the outer layers of a tree's trunk, and if it is girdled by damage the tree is dead.
So what caused this damage? Looks to me as if it is mechanical damage as most foot-rots start at ground level.

Well, the roof rats may, indeed, be the cause of the demise of your tree. I see a large amount of bark chewed off, which means the tree may have been girdled, thus cutting off the supply of nutrients traveling up to the tree's canopy. I agree with Mike, here (citrange). It could also be due to Phytophthora infection which can cause foot-rot as Mike mentions, as well as traveling up the tree (the odd discoloration on the branches and bark). Whatever caused the bark damage at the base of the tree (roof rats, a weed whacker, sprinklers hitting the trunk of the tree and the bark simply rotted and fell off) are most likely the cause of the death of this tree. The other concern I would have is how close the tree is to your house and roofline. You are providing those roof rats a clear path to your roof, and thus your attic. Which is where they love to live. We have a serious issue with the Norway rat (also known as roof rats or citrus rats). I would make sure you remove all trees or vegetation from the sides of your house the provide a "ladder" to your roof. Plus, the roots aren't good for your house's foundation and plumbing, either. Set traps or bait stations around your house to reduce the rat population (they carry disease as well as damaging your fruits, and what you're seeing with your lemons is clearly rat damage. They eat the sweeter skins of your sour citrus, and will hollow out the insides of your sweet citrus - classic rat damage). They are unhealthy pests, and you need to get rid of them. Bait stations can be set with non-kill through bait, so you do not kill birds of prey, just know that there is not antidote for that type of poison, so don't let dogs or small children get into the bait stations.

Patty S.

I live in the North Berkeley hills and, minus the rats and termite treatment, had exactly the same situation. My tree now looks exactly like your May 2014 photo, and the timing and symptoms were identical. Photos of the bark are also the same. I wonder if there is some local virus or other disease. I haven't seen any mites.

No virus, unlikely (although a long shot could be Triteza). But far more likely Phytophthora. Nothing mysterious about it. If your tree gets girdled from foot rot, and the bark is damaged in the same manner, it is akin to strangling a person. Pretty quick death.

Patty S.