The lack of structure sounds like MBD (metabolic bone disease). This results from insufficient calcium, when the animal doesn't receive enough calcium it metabolizes the calcium stored in the bones. This results in weak bones.
In alligator lizards, MBD usually first manifests itself in weakened jaw strength. It then progresses, and the limbs seem to bend under the weight of the body.
Ultra violet / UV light enables lizards to sythesize the vitamin D3 needed to properly metabolize calcium. I've had success / no MBD even without UV lights, but I now utilize them just to be safe. I dust all food items with Rep-cal with vitamin D3 and Herptivite.
Have you been supplementing? Do you use UV lights?
I noticed mild cases (slightly bent limbs) in some of my young leopard geckos when I was using another brand (can't remember the name) of calcium supplement. Rep-cal and Mineral indoor seem to be the best regarded supplements.
I've heard of people using turkey baby food to successfully rehad severly malnourished leopard geckos with poor appetites. This may work for your al as well. Mix in a generous amount of calcium, especially if you suspect MBD. See if he will lick it from an eye dropper. Be very careful if you try to force feed, as weak bones will break very easily.
By the way, what kind of alligator lizard do you have?
-Alice