Well I received my console back for the 2nd time and this time everything appears to be working, I was able to set it up last night and make it through update process.
For some reason installing Forza Horizon 2 again took forever, it stalled at 38% (and this is from a disc), I restarted the Xbox and then it finished the install just fine, but then syncing my data afterwards from the cloud took another hour. Yeah that's 2 hours to install one game, painful after not have a console for 50 days.
I also managed to reinstall Minecraft and the DLC I bought for it. I still have to install Madden 15, Dragon Age, The Crew and Destiny and sync all of the data, hopefully they don't take near as long as FH2 or it's going to be a long week.
And finally, I made sure to change the settings, disabled the auto-update feature, by selecting the Energy-saving mode, it disables the auto-on feature and pretty much everything else.