If you want to swap L/R on the phone then try "3DSteroid Pro". It does many of the same things StereoPhoto Maker does and you don't need a PC to run Windows.
I have been using 3DSteroid Pro for the past week to swap L/R (and save 'cross-eye' stereo jpegs for upload to G+ and FB) and also to auto-align my images. It seems to do a very good job. For input, it handles JPS and MPO and some other formats.