Hey Carl,
With the GE I always unbolted the exhaust at the head, disconnected the exhaust hangers and swung it aside. With the intake I usually leave the intake in the car but I think it's easiest to disconnect the lower half from the head with the upper half disconnected first... I can't recall if you can even get the lower half off without first removing the upper.
As for what could have gone wrong... A lot of things, really. The first could things I would check for are significantly distorted jackets in the head gasket, pitting (especially if it's close to the ring lands), warpage. Was this a composite or MLS HG?
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