@mrcool11: Start from the save if you want your choices. For whatever reason my save file is gone from my PC so I have to play it again, which sucks since the gameplay was so long and tedious the first time.

Just played through it, dosent to have anything to do with season 1 at all. Except for one reference that I can think of, but thats not about any player choice made in season 1. You can just play it.

I'd say make a backup of your entire walking dead folder (I like right-click, send to -> zip), and then figure out which is the correct prefs.prop file, move that to the correct place and remove all the others.

I posted about my save game issues for the original episodes here.