1. How do you prevent diseases from wild rabbits? Can you? Is there a vaccine?
I didn't worry about it beyond providing the right environment and nutrition. Oh but this link reminds me of the need for pest control at times..
https://herebunny.com/care/english-angora
I used the same permethrin based spritz as for chickens, the one I had was also labeled for use with rabbits IIRC, but please always do your own follow up research/confirmations!
2. Do you provide them with timothy hay and/or pellets while in the tractor?
This may depend on your pasture conditions and stock density. But generally speaking I would say yes hay and pellets are still a good choice to round out nutrition. I will note that angora goats required a higher quality (protein) hay than non angora goats.. so hopefully you will get some more input in that regard. Also my response is IF they're in the tractor full time.. If they stay in the tractor only in the day time.. then I only provide water, with hay and pellets being available upon return to the full time kennel. Rabbits also eat their cecal pellets. This link was a nice basic overview..
https://www.animalwised.com/raising-angora-rabbits-health-care-guide-1908.html
One of those links suggests alf alfa hay when "young" for the calcium content which I know is the reason to avoid it when older as it can cause urinary calculi. I don't know exactly when the cross over is or if alfalfa should ever be used.. (I have offered it in small amounts only as enrichment to my various animals)
3. Do you put wire on the bottom to prevent them from digging out?
The other poster mentioned great concerns.. if you don't screen the bottom.. they'll be gone! (if they're left in the same place very long or over night especially). I used 1/2 inch hardware cloth under the hutch I didn't move. On the open daytime pasture part (about 20x40 ft).. I placed a skirt along the fence (inside and out) because I knew they wouldn't back up to dig out.. but they did still dig in the middle of the fenced pasture and quickly became very long and deep with no way for me to retrieve them and only a matter of time before they popped out somewhere else, possibly even inside my pole barn.
When I first started tractor-ing my rabbits (different breeds does effect behavior slightly) for a few only a few hours per day.. they hadn't yet become obsessed with digging and so I was able to contain them easily enough. Once moved out full time.. it was THE most important and fun thing.
I don't see your location but will mention that heat can be a major problem for rabbits outside. My extended family when younger, used frozen water bottles with a fan blowing.
I know you said you already know how to care for rabbits in a traditional set up but this is still a great link for tons of rabbit information.. including available vaccines or health concerns..
https://rabbit.org/category/health/
For
me.. moving the tractors daily or several times per day was not ideal for any of my animals I've tried it with.. and I far prefer permanent set ups.. finding them ultimately easier to clean and maintain at any cost in addition to the security.
Cupcake (f) known as Thumper said to be mean by staff and Oreo (m), were sent home unfixed from my county shelter for an adoption fee of $5. My local vet wanted $400 each. Pub.vet (that's pub dot vet) took care of us during a spay/neuter clinic at the local tribal center for about $100 total. Cupcake did box me a couple times and preferred handling on her own terms but quickly settled into being a great pet. I learned rabbits aren't for me (at this stage in my life).
Anyways, I hope sharing my experience will give you some ideas. Overall it was a fantastic adventure, and I hope yours will bet to!