I wouldn't worry too much about drainage if you're on a hill. Just let them dig and see how it goes.
Definitely protect your trees from the buns. Mine killed all the trees in their enclosure. Who knew?
Sounds like you've covered everything I wish I'd done :)
Have some hidey-holes for them, like scrap plywood leaned against a straw bale, or old dog crates, or similar.
They will almost certainly kill the hardwood trees if you don't protect the trunks by fencing the rabbits away from them...
My colony is a 25'x25' (more or less) pen on bare ground. I put out hay or straw when it gets muddy and once or twice a year I pitchfork the old hay into a wheel barrow and put it in the garden.
I'd like to have three pens, so that one lies fallow all the time. I think that would be enough...