Similar to the idiom getting your panties in a bunch, I will hazard a guess that jimmies is a complementary masculine phrase. Jimmies may have originally referred to the male member (or accompanying anatomy). At least one instance occurs in the December 2003 issue of Men's Health.

We put our lives in their hands and our jimmies in their grip.

In the article, "in their grip" refers to wearing a condom.

As for rustle, this definition seems likely:

to act or move with energy or speed

This is just one example of getting your X in a Y or getting your (noun) (verbed) (e.g. getting your titties in a twist, getting your biscuits flipped, and so on). The gist of these expressions is that one is annoyed, angered, or upset. The severity or crudeness of the language may describe the intensity of emotion felt by the "rustled".

Jimmies works as a malleable, polysemic construction. Since it can mean nearly anything, the phrase can be employed in multiple situations, increasing its popularity.