Were they really on the island? Yes - they were transported to the childhood home by some unspecified means accessible to Euros
What happened to Molly? No bombs, just emotionally wrecked
. I hope Sherlock found her afterwards and said he loves her as a friend, or something.
Did the governor really kill himself? Yes
Who cleared up Mycroft's puke? Maybe he dry retched, maybe it was a prison lackey who cleaned it up
How did Moriaty get all that sorted out after just five minutes? After she gained control of the prison I think she had Moriarty over for visits on more than one occasion.
If Watson had chains round his feet, how did he get pulled out? God knows 
Who chained him up? Presumably Euros