The OpenSees Community

Charles Chadwell, who is now at Cal Poly, has done work on this.

i don't know about the geotech questions.
about the slowness of 2.0, you may have downloaded when Frank accidentally posted the debug version.
Download it again, but make sure you clear your cache first.

you should update to the latest version.
also, i don't know much about soils modeling.

look up the Region command, with this command you can assign demping to a specific region, such as the beam.
also, the reyleigh command assigns damping only to whatever elements have been defined up until that command, so you can do it that way, too.

good job.