pic 1 left, low oil pressure sending unit
pic 1 right, starter
pic 2, alternator
pic 3, vvtl solenoid near the oil fill cap
pic 4, these connect to the coolant loop and warm up the TB in cold environments.
One side connects to the head port in that pic, the other connects to the tee section of the metal line that feeds from the back of the block. There is supposed to be an inline tstat in there too.
pic 5, block coolant drain
pic 6, cute, but probably jail bait, I'll pass...
First off, WOW that is a messy looking engine. Your wires seem like a mess in the background pics.
The easy ones, the two ports coming off your throttle body are for coolant. The port closest to you (If I remember correctly) goes from the overfill tank to that port, the port closest to the motor goes to the motor. It is used to heat up the throttle body.
In terms of your plugs, in the first photo you have two plugs, I believe one of those goes to your Alternator and the other goes to your VVTi controller. I believe the left one is your VVTi (if not, then it is the 4 prong plug that is your VVTi) and the right one is your alternator.
The fouth photo I am not sure, but did you plug in your throttle position sensor? It is located on the back side of the throttle body in the bottom.
The stud, I have no idea.
And the last photo, plugs into the front seat of the car after you have it up and running.
This is the best I can do for now, I will be out looking at the engine bay later on this afternoon, so I can see if I can confirm any of these for you, if someone else hasn't.