The one that could damage the logic board is screw 1, the other 2 are going into the back of large ones underneath. Screw number 2 (red), I think is slightly longer as it long through both plates. If I doubt I would start with the shortest screw for number 1 and go from there.
A few thing worth trying:- Try turning off all auto sync data and iTunes match Try removing authorised account and logout of iTunes store. If you get no luck with that maybe try using a different computer with a clean install of iTunes. Hope that helps