Sounds like you think the experiment failed. Did you plant a seeded variety of buffalo or sod?

I don't think that was thatch. I think that was buffalo grass plants. Thatch is a dense mat of plant material just above the soil. It ranges from roots to stolons to grass plants. Yours didn't look like a dense mat of anything. It looked like grass in a dormant stage.

In the wild, buffalo grass would NOT be closely grazed by bison or cows. If it was grazed at all it would be grazed once in the spring and the bison would move on looking for tender new grass. They would have kept on moving until they reached central Canada and then they would have returned feeding on other grasses. By the time they returned to your buffalo grass patch, it would be 18 inches tall. The only time forage is closely grazed over long periods is after fences are installed to keep the livestock from leaving to look for fresh forage. Fencing animals in is not natural or "in the wild."

What is your watering schedule? How long and how often?

Is the blue grama an experiment or do you have reason to believe it is the solution to a problem?

Experiment is/was a success. I overseeded with the Blue Grama just to get some of the cute seedheads for the quail and other birds if possible.

The lawn was plugged with UC Verde clone (seedless) in spring of 2009. It's greening up now that we have warm weather and I've applied some water.

Normal watering schedule is explained here - I usually wake it up with a couple of closely spaced waterings, then go into summer schedule.
http://lazygardens.blogspot.com/2010/06/calculating-buffalo-grass-watering.html

It had a big buildup of dead stuff, dead Bermuda and other stuff at the base of the plants, and clumps of dead stuff making bare spots. What I was raking up was 90% dead and dry.

Buffalo did graze down to the nubs as they passed over grasslands. By the time the huge herd had passed there was a sort of bald strip littered with buffalo chips, with a border of less grazed grass. . That's how the buffalo hunters found them: find a grazed strip.

Here is a link that might be useful: All the Buffalo Grass Posts

Buffalo chips are a modern thing, too. Back then the dung beetles swarmed every morning and cleaned up the chips as fast as the buff moved away. 24 hours was max life for a dung pile. The modern miracle drugs used for deworming livestock kill dung beetles, so you see a lot more piles and a lot fewer dung beetles. But yes they grazed it down to nothing unless the wolves, lions, bears, or humans chased them away.

I don't think you needed to rake up anything. All that sounds very normal. Raking is good exercise, though.