Do you know what medication they prescribed for the Coccidia?
You can definitely switch him to a different tank while you clean his old one. You can use paper towel for now as substrate until you get something more permanent like tile if you want. Even when he's off meds and all cleared from parasites, you'll still want substrate that's easy to sanitize or else he'll just get reinfected after a few weeks again.
He'll probably be cranky! Haha you can still hold him for cuddles, but I wouldn't let him run around until he's better.
I use this probiotic:
http://www.beautifuldragons.com/Acid.html
It's a lightly sweet liquid, so many dragons will take it on it's own. I love ordering from her because every purchase supports her dragon rescue! For the probiotics, make sure to give them daily for a few days before starting meds, to get his good gut bacteria built up a little. Treatment should look something like this:
Week 1:
Monday: Give Probiotics first thing about 1-2 hours after basking, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Tuesday: Give Probiotics first thing about 1-2 hours after basking, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Wednesday: Give .11ml Fenbendazole first thing 1-2 hours after lights on, Probiotics about 1 hour after meds, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Thursday: Give Probiotics first thing about 1-2 hours after basking, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Friday: Give Probiotics first thing about 1-2 hours after basking, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Saturday: Give Probiotics first thing about 1-2 hours after basking, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Sunday: Give Probiotics first thing about 1-2 hours after basking, 1 hour later offer veg/salad, offer some lunchtime buggies, 2 hours before bed offer dinner buggies
Week 2: Repeat Week 1
Week 3: Repeat Week 1
Week 4: No meds or probiotics
Week 5: Begin Coccidia treatment!
Always offer salad first to entice them into eating it. Most dragons won't eat, especially babies, if filled up on bugs! And he's young enough to still appreciate two daily feedings. And get a kitchen scale to weigh him weekly so you can up or lower the Fenbendazole dose as needed. You'll probably need to increase it just because he's a baby and will likely gain weight quickly!
Oh! And I mix all of my dragons meds with a pinch of this:
http://www.beautifuldragons.com/Pangea.html
And he eats them happily! I don't like forcing meds and mine won't lick his on his own, so I mix a bit of Pangea and he goes crazy for it! He also started refusing his probiotics after a few days, so I mixed it with a pinch of this and he guzzled it down. I always highly reccomend it. It's good to have in your emergency kit for when you need to give meds, probiotics, or when they go off food and you need to syringe feed them. It also has bee pollen in it, a wonder supplement. It's the only substance in the world that contains every element in the human body. Essentially an all-natural multi-vitamin and super drug. Also helps immune system function. Bee Pollen contains at least 22 amino acids, 18 vitamins, 25 minerals, 59 trace elements, 11 enzymes or co-enzymes, 14 fatty acids, 11 carbohydrates and approximately 25 % protein. Bee pollen is extremely rich in carotenes, which are metabolic precursors of vitamin A. It is also high In B complex and vitamins C, D, E and Lecithin. Pangea is an excellent secret weapon
It's from the same place as the probiotic, so you can just do one order and get everything you need to make your little guy healthy, plus buying from her supports rescued dragons. Everyone wins!