It looks like electrical discharge. The larger "ball" that you saw flying across the screen looks very much like ball lightning. I've slowed down the video to 50% original speed. At that speed you can see many more discharges occurring around the cone of the tornado.Starting at about 1:50 in you can see more, less pronounced discharging. The discharge in yours occurs at about 3:39, but I am not sure if slowing it down helped a whole lot here. The video already seems cut down by YT's great flash video formatting.

There seems to be discharging through out the video, but I hope this helps you see it just a little better.



Being that such high voltage potentials have been seen on smaller dust devils, a tornado of this magnitude should easily be able to produce it's very own high voltage discharges. Here are a couple links to a few places that people have done their homework on the subject:

[link to www.thunderbolts.info]
[link to www.thunderbolts.info]

Because of the electrical potential that exists in some of these storms, cloud to ground, cloud to cloud, and the normal versions of lightning that we usually see are not the only things occurring. I'm sure any number of videos from this storm that these can be seen. This one makes it easy since the video was taken so close to the main potential of the storm near the vortex (which is arguably still electrical; yes the entire tornado).