Honestly, no matter where you take a raft on the Ark it's going to be super boney right now. The Milk Run tends to be worse then most because of the islands and splits in the channel. However, the commercials are still getting down it, so it can be done. WA to Ruby is the best access for the Milk.
Salida East to Rincon is probably a better option. It is going to be shallow and boney as well, but gets floated much more often at current levels. Another stretch you may want to look at is Trading Post to Texas Creek in the Bighorn Canyon.
Below the whitewater park in BV the river is generally II+/III-. It's read and run similar to the inbetweens in Browns, other than the Silver Bullet. Here is a photo of what it looks like at current levels: