With a jet boat you're connecting two fixed points with a joint that has no tolerance for longitudinal mis-alignment. The engine and pump don't have to be perfectly parallel, but the centerline of the crank and the centerline of the pump must intersect at the center of that double cardan joint. The way the case of that DC joint came apart, I'm pretty confident it's an alignment issue. I know I'm new to this forum, but I've been working on all kinds of shaft driven industrial equipment,farm equip, well heads etc. for almost 40 years and that looks like alignment to me. It's too bad somebody hasn't adapted a Dodge coupler (nothing to do with the auto maker) to a jet boat. They're perfect for imperfect alignment applications and absolutely constant velocity.
BlackSheep-- I was reading about your boat/engine build on another thread. Love it! I have built a couple hi-perf 460's over the years and am a fan of those (385 family) engines. With a set of cleaned-up (exh port) D3 heads and about 10:1's you can build a real torque monster.