2010 SKS System

The SKS system is only active when the car is turned OFF. Once you unlock the car and get it started, SKS is totally silent. So it's a very poor candidate for causing headaches, etc.

My guess is that you're having a reaction to the plastics offgassing in your new car. About all you can do about it is leave the windows open as much as possible and wait. There are a few new plastics used in the Prius that were just introduced in 2010, so they may affect you differently than in previous cars.

As for EMF, the Prius is actually lower than several other cars. I think it was a Chevrolet Cobalt that really pinned the meter on EMFs.

Relative to the potential for EMF biological effects, that's a can of worms that can get you accused of all sorts of deviant beliefs. There's a book by a university professor describing the damage done by the introduction of AC power about 100 years ago. I haven't read it, but it would be interesting to see what he turned up. I regard the effects of non-ionizing radiation on biological systems as an inadequately studied area.