Did you check the motor mounts? If the engine is moving around it's going to be putting all kinds of stress on that manifold. It's not uncommon for the lower mounting bolts to loosen up, causing the upper mount to break.
Also, like 91warrior just mentioned, it is possible to install it upside down which will put undue stress on it. If I remember correctly the top of the manifold has a reinfoced bridge, and an arrow to indicate that it is the top side.
Other than that, i can't see what would be causing it unless you're slamming the pieces together, if you're twisting it and forcing it when you put everything together that could be the culprit. I'm sure you won't be doing that though, by now you realize that the manifold is weak.
The manifold just isn't the strongest design, it's aluminum throughout except right in the center part which creates a pinch point where all the stress gets focused. I went through a couple on my warrior. The first one was the original one so that wasn't a surprise, but the second one only lasted a couple months so I think that was a faulty part, it also wasn't an orignal yamaha part.
