It's probably time to open a Case with Technical Support, providing your model (or a simplified version that reproduces the issue) - if you can.
There is only one report in our database about an issue where strain energy calculation hung and it had to be software fixed for Wildfire 4.0.
And the "Mechanica model save error" sounds like a session corruption happening during the engine run.
Nothing to say against continuing with finding a workaround, though ...
Just make sure to keep all roads open.