I'll take a guess, having spent a couple days thinking about those handles. One possible reason for the large handles is to provide a better purchase by someone of small stature sitting in the pilot's seat. Those small handles on the cockpit-ends of the rods might be enough for a strong man with big hands to pull, but they're in a poor position for someone with a small stature to apply much force. Think of where you'd be putting your hands and arms to pull on those small handles in an emergency - your left hand is on the wheel, you're seatbelt is tight, you're dividing your attention between flying the airplane and reaching with your other hand to pull on the little handles, which are about shoulder-height on the same plane as your seat-back, and a bit more than an elbow distant from your shoulder. If you're sitting in a chair right now, reach for that location - it's really awkward, and you have little leverage to pull with. The long handles further back might be just where AE could reach back and "straight-arm" them. Try that while you're sitting down - stick your right arm straight back just below shoulder level and make a fist. That's about where those handles are located, if the "someone" has short arms. The three distinct angles might also be intentional, to make it easy to tell which handle you are grabbing without looking. Reach back, grab one, and lean forward while rotating your torso to the left, and you'll be able to pull with a lot of force.
This still doesn't explain what the rods did, but the above description sure sounds consistant with emergency dump valves to me.
I see that the handles and rods are on the Harney drawings. I also can see the rods barely visible under AE's elbow in one of the photos on page 2 of this thread. It still isn't clear what they connect to, but I'm hopefull they'll show that detail in some unexpected photo.
Does anyone recognize the small handles from any other aircraft use? The look tantalizingly familiar to me...