It sounds like much of what you are doing is right. For some more details that may help see
http://www.askmehelpdesk.com/dogs/in...tml#post251809 Certainly working with the vet to clear up the cococcious and worms is the right thing to do. You won't get far until he has a normal stool. Continue to work with the vet. The grid I suggest in the sticky isn't near as effective with bowel movements.
Follow the usual recommendations, leaving him little more room than enough to stretch out in the crate. When you take him out for his last trip at night, be sure and walk him around enough to stimulate his bowels so he empties them completely. Most of my puppies have been able to make it through most nights by 11 weeks. Once you have cleared up all his problems, he should be able to also. For the next week, you may have to set the alarm for before he has been waking you up and take him out. You do want to stop him from fouling the crate before he loses his natural aversion to his own filth. It is very important to keep the crate clean.