A picture of the trunk would be more useful. From your description I think the rampant thorny branches are likely to be rootstock and should be removed as they are taking the nutrients from the graft and the fruit. Citrus grafts are usually higher on the trunk than other fruit trees. Al

Just to add a bit, you may wish to wait a bit before cutting any questionable sections. In Danville, my lemons have re-sprouted leaves on branches that had a bit of brown. This week i will be cutting the moldy, light brown and very dead branches, but any questionable ones i will wait another month or two. On a different note, i just noticed my (previously 5 ft.) V.Pink Lemon in Napa push a nub 1/2" above the graft line. I think it felt me me wanting to dig it up and it responded. - ha! [now hoping my Bearss Lime will do the same] That December stretch of 10 18F-25F nights really surprised me as to what was killed and damaged... and which area of the yard too. I do plan to post pics of the recoveries. -George

th102 now is not the ideal time to prune your tree. Having said that. It will still leaf out and produce fruit if you prune it now. The longer you wait the more sap will be flowing thought the tree and the tree will lose more of its energy due to losing more sap. Keep in mind that pruning while the tree is no longer dormant will be a shock to the tree. Thus it will likely appear to stop the active growing process for 1-3 weeks. Your fruiting and ripening cycle this season will also likely be delayed/slowed by roughly the same amount of time.

Don't prune them; maybe after you start to see new growth. Meyer lemons are more of a bush than a "tree"; so the only reason to prune is for shape/esthetics. Commercially, and in my garden trees, I prune out any downward growing limbs, anything touching the ground, and any limbs crossing the center (opens up the centers for more sun)