Keeping chickens often comes down to your philosophy of choice ( and a few other things).
What do I disinfect with? Nothing. Never done it. I CLEAN my hen house, shovel out the poo when the smell is obnoxious (sooner is better) as that ammonia irritates the eyes and lungs of your birds. Unhappy, uncomfortable birds can become sick birds, so avoid it and keep the hen house clean and dry with ventilation but not drafts. ( I have often thought that piece of advice sounded dumb, ventilation but no drafts, right, how does that work?)
Vaccination? Never done it. Do not even feed medicated starter to my brand new chicksm either layers or meat birds. What I DO do, is make sure that all chicks I get are warm, but have a place to get out of the warmth if it is too hot. Over heating and over cooling are both problems for chicks, make sure they can come and go from the heat as they see fit. I make sure they are not subject to drafts. Provide clean water, fresh feed and dry bedding. BUt no vaccinations ever.
Supplements or vitamins? If I have some chicks whom I think have a particularly delicate constitution, I give them Poulvite in theri water for a day or two, but that is it. I find that Poulvite quickly turns funky and slimey in the waterer, so do not let it go more than 2 days without washing the waterer out. What I like better is to buy a bottle of cod liver oil capsules, jab a hole in a capsule with a pin and while performing a manouver that requires 6 hands and an assistant, give each chick a glop of cod liver oil in its mouth. THey do not enjoy this handling, but it's good for them. The cod liver oil, maybe not the handling.
When my birds develop coughs or sniffles, I let them have coughs and sniffles. I have learned that some thngs birds recover from and I give them the chance too. THe things that birds don't recover from often kill them quicker than I have time to react to. You want birds that are healthy enough to survive the odd germ.
There is lots more you can read here on WCPS in old posts about roost height, heating hen houses, water in or out during winter, bedding choices, nest box size and style..all sorts of things that might help you be more successful next time around. But overall I would suggest that you not treat chickens like they are made of fine china. Do everything within your power to provide what they need for optimum health, protection from the elements and predators. BUt after that, some of their survival is up to them and over fussing can leave you with weak birds that do not handle adversity well. Good luck...you'll get it figured out.