I've slowed the WLD on my Meyer Lemon down pretty good now (I lose a few older leaves every once in a while but it looks like the newer growth is hanging in there). I lost about 50% of the leaves and am now able to see the branching better and have noticed alot of crowded branches and a few that are crossing. I know that pruning is generally avoided but was wondering if others typically clean this up or just leave it. If pruning is called for, is it best to wait until it starts leafing out again or do it now (or some other time)?

If a branch has no leaves, therefore the branch is not producing photosynthates for the tree, and if the branch absolutely must be removed, than it really does not matter when it is removed. I've always followed the practice that branches to eliminate, is based on the concept that any space within the tree's canopy must be covered by only one branch. It is not convenient to let surplus branches occupy the same aerial space. Anyway , thinning must not deplete any sector of the canopy, as this reduces fruit production. It is important to note that during the first years of a tree's life, there is no need to cut at all, since research has shown that any cut to a young tree reduces root growth. This is due to the equilibrium between the foliage and the root system. A- Millet

The best time to prune is when you have rootstocks ready to graft on.
Good gift for friends and good practice grafting.