Rivendells are designed mostly for a back rack if you are carrying any real weight. Depending on what you want to carry, will help determine the rack you want. I have that same bike, with a front Nitto Mark's Rack and a Wald basket but it really can't handle much weight. This week I was carrying two Kryptonite Fahgettaboudit locks in the basket and the steering and handling was sketchy at best. I am now thinking a Nitto Big rear rack is what I will get.
Tires, keep what you have if you can fit them with the fenders. Again I use SKS fenders with Marathon 42's and they work just fine with plenty of room to spare. The smallest I would ever go is 38's but again your call on what you are comfortable with.
The black brakes I could live with but if they are anodized then that can be removed with strong oven cleaner or lye mixed with water. I have done this successfully with cranks and stems.
It is a great bike, but I am biased.