Looks fine from what I see in the pics.
Did you rotate the wheels by hand? Any noise from the wheel bearings or rear when you do that?
Just wipe out the bottom of the housing with a rag to get out all the sediment.
Put the cover back on and fill the rear from the side plug. It's a round threaded plug with a 3/8 square recessed head. Use a small 3/8 extension and ratchet to remove it and fill with gear oil until it spills out.
Then pull the driveshaft and inspect/replace the u-joints. That where my money is at for vibration you are hearing.