I would second the pumphouse run. Canoeing the colorado from pumphouse down was the beginning of it all for me.
You can start at pumphouse, go down to state bridge camping on river left, only rapid of concern would be yarmony. Second leg would be from state bridge to Jack Flats. And third leg from there to I-70 at dotsero. I cant remember their exact locations but three other rapids would cause problems; rodeo, pinball at Bob's bridge, and some other that just submerges the canoe in a huge wave train - but is avoidable.
All in all it is like 60 miles, could do it in 2 days in high water, you will flip.. but its alot of fun. Just cause its a canoe don't take it lightly.