My puppy with coccidia poops in his crate, now that he’s getting better how do I retrain him to not use his crate as a bathroom?

Hello,

I'm a first time dog owner, and have just recently purchased a Morkie (Maltese/Yorkie cross). As to date, he is 14 weeks old. A week after I brought him home (6 weeks ago), he was diagnosed with Giardia. Unfortunately, the vet I brought him to was incompetent, and gave me the wrong meds. After finishing those meds and not seeing any improvement in his diarrhea, I brought him to another vet, and that's when they told me he not only had Giardia but also Coccidia. He has 2 more days to go with these new meds, so hopefully it will work.

My issue is that because this has been dragged on for so long, and since he has been having diarrhea for practically his entire lifetime (not all the time...sometimes the stool would be firmer like soft-serve icecream), that this has hindered his crate training. He is very smart and learned to go to the door and scratch whenever he needs to "go", by 9 weeks. However, when he has diarrhea, he is unable to hold it and goes in his crate overnight. Since his poos are so sparadic due to the diarrhea, I cannot anticipate when to wake up at night to let him out.

Lately, he's had about 2 accidents in the crate, but they seem more solid than usual (I do not think he had diarrhea). My fear is that even when he doesn't have diarrhea, he feels he can go in the crate. I'm scared the parasites have hindered his crate training. How do I re-train him when he already has the mindset that it's okay to go in the crate?

Please help. Thank you!

P.S. I've read that you suggested a few people to make their dogs be outside dogs for a while (for those dogs content in pooing in their crate and lying in it). I live in Canada, and our winters are harsh. I can't do that. It's summer now, but it's been raining relentlessly. I do not feel confident leaving a little puppy outside. That, and our backyard is not completely fenced off, so I'd die if someone ever stole him.

Sincerely,
Evelyn