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Puppy parvo survivor diagnosed with giardia, need help!

I recently rescued a puppy who is a survivor of parvo, he is the only one out of 5 of his siblings that survived. He is currently 5 months old and 9.7 lbs, yorkie poodle mix, and has been diagnosed with giardia about 3 weeks ago. They prescribed him a round of panacur, followed by a round of flagyl, both of which he completed. They also insisted on feeding him Hills I/D prescription diet (sensitive) Rice & Egg formula. None of this seems to be working. His stool is mushy and greasy looking (no chunks of mucus like it was originally), he has shown a huge increase in shedding, and seems to be very itchy and biting his paws on occasion. They now have prescribed him another round of flagyl (metronidazole, 100mg). I am at a loss, I typically take a more balanced approach between holistic and western medicine for both myself and my dog. But the vet seems adamant about staying on track with this food and medication. Does anyone have any suggestions? I am convinced the food has worsened the condition of his stool but i am also bias as I only give my dogs USA “human grade” premium foods, I also used to cook my previous dogs food (of course mixing it with a number of plant based supplements). Either way, I really am not sure what to do, I am so scared my little puppy is going to worsen, he has been through so much already, any input is greatly appreciated!

Also, we do have him on a probiotic called Synacore Digestive Support (Van Beek is the brand) + a chewable digestive enzyme (which also has a probiotic in it) the brand is NaturVet.

This is my thinking… his gut is one big swamp due to the effects of parvo (I assume he must have something similar to SIBO as he shows many of the signs). Now, in this swamp he has nasty parasites (giardia) eating away at his already vulnerable gut. This being said, after much research this is what I was thinking of going, but am nervous as none of these remedies are FDA approved for dogs (i of course will check with his vet but i find that many times hearing other pet owner’s experience is much more beneficial as every dog is different).

-take him off the vet food. Cook him organic, no antibiotic/hormones, vegetarian fed (aka the best of the best) chicken + sweet potato + carrots (i heard carrots help with a dogs digestive system).

-now for the basic supplements any puppy or dog would need in his food, I would mix in: seaweed plant based calcium powder ( https://www.amazon.com/Animal-Essentials-JX0001-Seaweed-Calcium/dp/B0002AAO2M/ref=sr_1_1?ie=UTF8&qid=1472224097&sr=8-1&keywords=seaweed+calcium+pet ), and Multi-vitamin – this vitamin contains small bits of garlic and yucca which could help his intestinal problems ( https://www.amazon.com/Animal-Essentials-Herbal-Multi-Vitamin-Dogs/dp/B010F36XRK/ref=pd_sim_468_5?ie=UTF8&psc=1&refRID=7T75QBGRD5NZPA4GD5AJ )

-now for fighting off the giardia, building his immune system, and dealing with the aftermath of the parvo, I would add the following to his homemade food: goldenseal, echinacea, grapefruit seed extract, and slippery elm. (here is the article I read that suggested these items: http://ottawavalleydogwhisperer.blogspot.com/2012/04/diarrhea-in-dogs-puppies-cats-kittens.html )
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