Ok, iPhone is fixed and working. Honestly, I think it was just a waiting and time thing. I spent 5+ hours last night doing everything from turning off security, trying different versions of things and every other possible thing I found on the web.
I decided to just do some work today and keep iTunes running and my iPhone plugged in while doing everything. My phone would reset on it's own every once in awhile. I was having Chrome issues and restarting my computer randomly. Then suddenly a message popped up saying that the iPhone was in "Restore mode" and needed to be restored, about 15 HOURS LATER. I restored it and then choose my last backup when they asked to restore it. It has taken a few hours (I have the 64GB, with only about 10GB free) and I still have a little bit more to go for everything to be synced.
It calls, messages, al folders are in place and everything seems to be fine for now. Sooooooo, in the end it just seems like keeping it plugged in worked. I saw some people had similar experiences, so it may just be time in the end.