Head, Arms, Lower Legs: 25th Storm Shadow
Torso and Upper Legs: 25th Flash
The G.I. Jonin showed up in a handful of panels of the Transformers vs. G.I. Joe comic book. Intended as a more controllable replacement for the Joe Team and commanded by the Jugglers. Seeing as a few pages later General Flagg has ousted the President of the United States, it's not a plan that works out for the Jugglers, but it inspired some customs at least.
I have a ton of 25th Storm Shadow parts in my fodder bins. While I didn't have as many of the Flash parts they aren't terribly versatile either. So a set of customs that allowed me to use up some of that fodder was welcome. That they were a concept I thought was pretty cool was a nice bonus.
In my 'verse I figure that after Storm Shadow broke into the Juggler's chambers they decided the best way to defend against a ninja was with a ninja. They tracked some down, offered them absurd amounts of money, and now they have a private ninja security force and dirty tricks team, with the American taxpayers footing the bill.