Turtle shell cracks.?

I have an african sideneck turtle who has always had a few shallow cracks in his shell, within the last 6 months he has slowly developed two pencil eraser sized deep holes in his shell. I apply iodine every night to the affected areas. I have also resorted to taking his water tub out of his cage so he doesn't bask in it all day. Instead I give him a one hour nightly bath to hydrate himself and eat. Any advice? The closest specialty vet is extremely expensive just to get him seen, I would prefer to treat him at home, and possibly reduce stress on the little guy.