I did Boquillas canyon 3 years ago and was blown away. I wanted to do the lower canyons (below boquillas) but didnt have the time; it can take a week if I remember right. Here are some places to get started.
The NPS site is pretty helpful
Big Bend National Park - Floating the Rio Grande (U.S. National Park Service)
I got my shuttle and rented a canoe from Desert sports
Mountain Biking, Rafting, Canoeing, Hiking in Big Bend, Texas | Desert Sports
they were very helpful and the prices were reasonable. They came reccommended from a long time terlingua bum that I know.
There are great guidebooks by Louis Albach here is the one for the lower canyons
Big Bend Book Store
If I remember the rapid ratings were geared twoards canoes so a class IV in this book is more like a class III or II+ on a colorado river.
We went in the winter and had great weather. It is too hot to do in the summer. I remember standing naked on the beach on New years day was a really great feeling.
Lastly have a blast. PM me if you have any questions about the park permit or other logistics.