The gold standard for diagnosing a PFO is transesophageal echo; another test, which can't diagnose PFO but can diagnose a shunt, is transcranial doppler. Given your story, I would be VERY curious as to what a TCD would show.
When I had my transthoracic echo, my doc asked whether I would be willing to have a transesophageal if he didn't feel he was getting a good enough image in the transthoracic. He didn't want to jump straight to the transesophageal because it's not exactly a comfortable thing to have. I said yes, but I guess he felt he could see everything okay in the transthoracic. I could certainly see the bubbles when they went through on the one side.
I hadn't really thought about the possibility of some other kind of shunt somewhere else. We always think PFO because they are so common. I think I would like to get a TCD, and with a history of migraine it seems like something worth having anyway. I've had trouble finding a doc that really cares enough to help me figure it out, and after the second hit lost the heart to keep looking. Hearing it happen to someone else and posting my story here has kind of rekindled an interest to start trying to figure it out again.
And thanks to both TSandM and chillyinCanada for the sympathy. It hasn't been easy, the initial recovery was quick but the rest is very very slow. I'm hoping it will slowly but surely continue to improve.