Several things can cause the manifold to break. Rain, as Scott said, along with the lack of supporting springs on the lower exhaust system. I've never seen a manifold break that severely.
The manifolds are mild stainless steel so let your welder know that. it will make a difference in the quality of his weld. If the old engine was blown, I would remove one of the heads and use it as my flat plane. Bolt the manifold back in place with all cracks closed as much as possible. The head warps on it's surface where it contacts the block. There's a little wiggle room for the manifolds to fit onto their studs and if there was enough head warpage to affect the manifold you would see a gap between the head and block, or if it warped sideways, it would break head bolts because they are a tight fit through the head as they pass into the block.
On a side note, before you install your 3.4, you should remove the pipe plug that's in the trunk side head just above the #5 exhaust port if you haven't already done so. Then remove the sensor that's in the opposite head, just above the #2 exhaust port. Put the pipe plug in place of the sensor and install a new gauge sending unit in the trunk side head. You can use your old 2.8 set up as a guide.