Brakes dude. Be VERY cautious of both dealers. I highly doubt you have 6 k in repairs. Do this, put the fluid back in the front and rear diffs, put the fluid back into the transfer case. I doubt you were in 4 wheel drive the entire time, you would have noticed, the 4wd light would be on, etc. regarding the mismatched tires, I doubt it was enough to cause any damage, was the car driven tilted? Wouldn't you notice? Plus I'm pretty sure it's an open diff up front anyway, someone can chime in and correct me.
I would take your issues one at a time and ignore the fearmongoring stealerships. If your diffs are damaged you can tell, they will grind, buzz, while your driving, or just grenade.