I wonder how the images look after map-projection. You can overlay them in stereo_gui or you favorite GIS tool. Hopefully they look comparable.
How about the low-res DEM itself, does not look smooth, without holes and noise?
One can also try stereo with the original (unprojected) images and --stereo-algorithm 2.
Then, a lot of holes can be a symptom of the images being too different, perhaps.
The process should work, the issue may be your daata. You could also try a different dataset as well, before returing to this one.