How do I become limber enough after having lived a life as a sedentary software developer & gamer so that I can bend like Gumby? 
I'm a ninja.
Step one: be Japanese
Hey guess what, you're probably not Japanese so you fail
GG
I'm a ninja.
Step one: be Japanese
Hey guess what, you're probably not Japanese so you fail
GG
http://www.imdb.com/title/tt1182921/ says otherwise
Well too bad, you can't.
You can, however, try to become a student at a Bujinkan affiliated dojo and learn ninpo taijutsu, which is anything but hype.
It's pain! Lots and lots of pain!
You claim to want to be a ninja, and the first thing you ask about is flexability?
How about years of practice, muscle memory, form, stance, technique.
Your query suggest that you have little if any knowledge of what you seek to attain.
Also the vast majority of the skills of Ninjutsu, were simply those of a catburgler/assassin. Most of these skills were specific to this trade, and would have little value in practicle application.
I suggest you demistify your goals and chose an open hand martial arts style.
F.....that was easy.:ninja: