I personally hate iPods so I dont mind if they all go up in a EMP.
But as to the cost and ease of making one. A small scale device could be made for about $3000 then chucked on a back of a truck and parked and detonated.
It doesnt need the pinpoint accuracy and other features your military has built into theres to be effective. There are simple designs that could be used and they may not be the best design but it doesnt mean it wont be effective.
Buying the parts would attract very little attention because nobody would be looking out for most of the components.

I think you are underestimating how easily this could be done with the right design.