Geezer, go to options, select player one(or if your player two) Lefty Flip, then just turn the guitar the way you would hold it (Right hand on frets, left on strum bar) and it is like normal.
im left handed but i play GH3 right handed. the lefty flip is ok and i didnt find the whammy bar got in the way. try strumming with your fingers and having the whammy under your thumb?