Sensitivities and Allergies

My puppy is 5 1/2 months, 62 pounds, and overall is doing great. However, he's been going through it as of late and I wanted to ask for some people's own experiences and advice. I'll try to keep it concise because he's had a lot of issues.

Since we brought him home in early October, he's had struggles with diarrhea. Initially tested positive for giardia antigens and we treated that. When that didn't stop his diarrhea, vet put us on Hill's Prescription I/d food for 3 weeks and that seemed to work. After we went off the Hill's, we went to Purina Pro Plan Large Breed Puppy Sensitive Stomach, and it seemed like that was working. In mid-November, his eyes got super red and droopy and developed green discharge frequently. Vet diagnosed him with general conjunctivitis and prescribed eye drops. He HATED the drops, so the vet switched us to NeoPolyBac ointment and he did much better with that. Eyes still seemed red occasionally, but definitely looked more normal. Vet told us we could get off the ointment, as his eyes are naturally red and droopy due to slight ectropion. He was off the ointment for two days when the green discharge came back. So we're back on the ointment since mid December.

Last week he had real bad diarrhea all week, we tried to switch to boiled chicken and rice and that only made it worse. So went to the vet again where we had a big meeting with the vet to figure out what the heck is going on with him. So, now he's starting Royal Canin hydrolyzed protein food, as the vet thinks that he could have difficulties digesting and breaking down protein. He can't have any other protein source, and is only allowed vegan marshmallows to take his pills and one fruit or vegetable. He's on this for 8-12 weeks before we can slowly start to introduce stuff back into his diet one-by-one. He also tested positive for coccidia, so we have medicine to treat that, as well as metronidazole to help with his gastrointestinal inflammation. He's also on Zyrtec as we think his eye problem could now be allergy related. Once he's on his new diet food for a week, we're going to stop the ointment and use artificial tear drops to see if some of his redness is due to dryness.

So that's all his issues. My question to other owners are, has anyone experienced something similar with their Berners, either puppy or adult? Did you have to stay on the hydrolyzed prescription food indefinitely, or were you able to figure out the sensitivity/allergy and switch off of it (to a cheaper food)? Has anyone dealt with similar eye issues and how was it resolved?