as the previous poster mentioned, putting the pivot point where the trough balances is the best, but that probably isn't going to be at the collector pipe. that will be determined by the materials used and how you construct the trough, as the trough will balance at it's center of mass.
You mentioned that your using a deep trough design. Such a design uses its material inefficiently. if the edges of the trough are twice the height from the bottom of the trough as the focal point, the edges are at 60 degrees. at the edge for an added inch of materials, you only add 1/2 an inch of sunlight.
for the opposite situation, the focal point is twice the height from the bottom of the trough as the edge of the trough, the edges are at 30 degrees. at the edge for an added inch of material, you add .8 inch of sunlight. With the focal point so high it is hard to put on a lid. So, in this case, you'll probably use a "glass" evacuated collector.
If you going to put a lid over your trough, to make the best use of your materials, put the focal point at the same height as the edges of the trough.
here is a link to more pics on the mit lesothos project: http://www.solarturbinegroup.org/media/
here is a pic of the pipe they used. From the picture, it seems like their pipe is only about 1 1/2 inch at the most. And, their trough is HUGE compared to yours. I would think you could get away with a pipe of only 1".
Not sure what they are using to mount the "glass" tube. what is that grey stuff and the red stuff. And why are they using a clamp?