Bottom left corner of your throttle body picture seems to indicate your problem. Looks like mud and water made it past the airbox seal or it came in from around the throttle body boots where they are screwed into the bottom of the air box.
After further review of both those pictures, you have alot of work ahead of you. You now have silt in places your not going to be able to clean out without alot of disassembly. Pinion bearing seals, diff output seals, subtrans external seals, wheel bearings, brakes, suspension joints ect are now full of that stuff. Pressure washing those places only drives the grit further in. Your going to be chasing issues with that thing for a while. Good luck