It looks as if something was left in the housing floating, like a nut or something. The gouge marks in the case are definately not normal.
There are 2 metal tabs that hold the brake line to the outside face of the Diff Cap at the top of the housing. Are they still present, or did one perhaps fall into the housing on dissassembly?
Also your fluid looks really burned on the bearing caps. I would recomend a thorough rinse with some break clean, and replace with fresh fluid.
You mentioned no RTV was used, did you re use the stock gasket? It is reusable, but definately worth replacing for 12$.
These also have a specific way they orientate on the housing, perhaps it's installed wrong?
Was there oil leaking from the housing, or low fluid in the housing when you checked it again? If you did not use a gasket or RTV you most likely lost fluid too.
Perhaps a tooth chipped ? Check your gears for any sign of wear or chipped teeth.
Something was definately in there grinding around. Hopefully a flush and oil replacement will solve the issue. I recommend the Royal Purple, or Mobil 1 synthetic.
2006 4x4, Standard Cab, 3.5L, 5 Speed Manual, 4.10's w/ Eaton Truetrac, Flowmaster Exhaust, K&N Intake, Optima Yellow Top, TB's Cranked, Gabriel Load Carrier Coil-Over Shocks (Front), 32 x 11.50 BFG MT's, Kicker 3-Way door speakers, Power Door Locks.