So I've been trying to learn how to play "Jane Says" on the guitar and I should mention that I've only been playing about a year now. That said, I noticed that Navarro mutes the Low E string right before he hits the A chord and then the embellishments. I noticed Duff did it too in the Guitar Center Sessions version as well.
Strum Here to see this.
I can't seem to do that without muting out the A string also.

I guess in time it will become clear without thinking about it.

~Roxx~