over a year ago:
I've just started the series, and only on book 2, but I've thought that all along. I'd be surprised if that's not the way it all went down. My only problem with your theory is with Rhaegar Raping her, I think they were in love. From all accounts Rhaegar was quite the catch, and Lyanna probably fell for him, so they ran off together and hooked up.
Also remember Dany in the Tower of the Undying, A Dragon has three heads, Jon is the third.