First: when creating back ups of your game, I personally recommend you export them instead of saving as (File > Export). You can rename the exported file without problems as far as I know. At least that's what I do. In my case, if I want to revert to an older version, I usually delete the version I was working on (backing that up on a case by case basis).
Second: you're getting an index out of bounds error, but it seems different from the old one from 4.0.1. It happens right as it tries to read your scene 0 xml file, so it seems scene related. I have one game that I did "save as" to, and I do get a pop up when I open it, but otherwise the game tests fine (I've been procrastinating to post about that, to be honest). Is this the same case for you, or is the game refusing to test at all? You could try opening all your scenes, then saving your game, and see if you still get the error.
Third: since it's an index out of bounds error (and if you can't test your game at all), you could try what's described here:
http://community.stencyl.com/index.php?issue=1552.0Lastly: touch controls and mouse controls are the same (they use the same blocks), so you could meanwhile work on your game testing in either Windows or HTML5, using the mouse to control it. At least until you can get help from someone more experienced with the mobile stuff.