We visited the vet today, and it seems that he has a calcium deficiency, and his official diagnosis was Metabolic Bone Disease. Just in the last day he developed a little soft spot underneath.
He got 2 shots; a Vitamin AD, and Calcium Gluconate, and sent home with 14 days worth of Calcium for me to give him.
He has been eating the Turtle Jello Shots for quite some time, but I was missing enough Calcium - I feel horrible.
He told me to get some feeder fish, meal or earth worms to add to his diet, dry dock him as much as possible to prevent infection, and stop the regular diet for now.

I feel like a bad turtle momma right now.