I've managed to put mine back together several times.
Very difficult but possible. I'm assuming that the universal assembly directly off of the crankshaft rear is what's popping off. Let's confirm that part first.
Also confirm that the rear truck wheel gear (singular, not plural) is properly engaging the face of the wheel and not sticking, hanging, or otherwise messing up; i.e. it runs with the driveshaft removed and flopping the rear universal around. If that tolerance is 'off' or the gear is worn out, another issue entirely.
The design flaw on these is that while actually driven through the truck gears and the worm, you're also transmitting torque through that driveshaft from truck to truck. If you have tension in either direction of travel through the shaft, it will spring something. That's what makes taking the trucks off next to a fatal error; mis-aligned with each other, they will spring the moving driveshaft apart repeatedly.
I always hold my breath running mine, and these guys that run them at 50mph on a layout have never actually seen a Shay.
It's an incredibly delicate mechanism, basically, a miracle when it works right and you can creep it around as it should be run.