I'm no expert in this either but my my reading of it is the danger is the bullets
(as MileHigh) put it and not EM waves: high speed particles from the sun or
from outside our solar system. I don't know why they refer to it as radiation
in the same sentence they say it's particles since when I hear radiation I
think of X and gamma rays which are EM waves.
From my reading and viewing, polyethylene is supposed to help with the
cosmic rays (high speed particles from outside the solar system) and
water or lead (though lead is too heavy to use) is supposed to help with
the particles from the sun. This seems to be an area of ongoing research
though. Polyethylene is used for the sleeping compartments in the ISS
for this reason. The document you linked to, 140.pdf, does mention
polyethylene. Here's a video that talks about these issues, even using
electric fields and magnetic fields to redirect particles away, parts 2, 3
and 4 in particular: http://www.youtube.com/user/synteticboy#p/c/23FC6C0288281BBA
NASA's Space Radiation Laboratory studies these issues: http://spaceradiation.usra.edu/
As well as humans, the electronics also needs to be hardened.
As for propulsion there's a new ion engine technology that's supposed
to be a game changer (so not use usual puny amount of thrust over
a long period of time.) It's already working on the ground and it'll be
tested on the space station around 2013 for reboosting. After that
they'll work on a version for a full scale rocket. They say it should be
able to use it to get to Mars in 39 days by thrusting the entire time
(same or less amount of fuel, just shoving it out the back faster): http://www.nautel.com/rocketscience/ http://watch.ctv.ca/news/#clip225583
So stuff's happening in the public world.