Set a new mark on this today, 5/3/11, at 8h57m. My GPS gave 36.3 miles for the whole thing from the Knowles TH. It occurs to me now you could save 2.2 miles by starting at the Mee TH & avoiding the Knowles TH out & back. For reference, my time to close the loop (w/o the out & back section) was 8h32m (from my GPS).
I started at 5:51AM, just when it was light enough. It was darned cold (below freezing), but warmed up nicely later. I found good water running the full length of both canyons. I didn't see anyone all day (Tuesday) until the spectacular climb out of Mee Canyon, when I caught up with Stan Wagon, the founder of Ultrarunner Magazine! He & his partner had visited the huge undercut in upper Mee. From the Mee TH, I cruised pretty well along the cow path back towards my car until taking a wrong turn near the stock tank 2-3 miles out & ended up navigating cross-country via GPS to get back on track. Oops! Otherwise, no problems with navigation.
I estimate that a little over half of the route is off-trail. That includes pretty much all of Knowles once you reach the bottom of the canyon, much of the way along the Colorado except near Black Rocks camp, and most of Mee except for an excellent trail for the first couple of miles after you leave the Colorado. Up top its mostly old cow paths.
My GPS track is here (gpx).
Here are some approx. splits:
Bottom of Knowles: 5.0mi, 1:00
Knowles @ Colo River: 13.8mi, 3:00
Mee @ Colo River: 18.8mi, 4:42
Mee exit: 26.3mi, 6:44
Mee TH: 28.8mi, 7:33
Knowles TH: 36.3mi, 8:57