il take a stab at a few things for you.
the hose in the first picture looks like the hose which connects to the head like this. not sure what the other thing is
the sump looks like oil drain from a turbo.
i cant really help you with the vacuum lines as i havnt done that on mine yet.
the orange and green plug is for water temp at the back of the head i believe. it can be seen on the far left of the picture i gave you above.
that line off the plenum may go to the brake booster fro vacuum?
not sure on harmonic balancer. it looks like an indicator mark tho?
the plug on alternator will be on your loom. you have the big plug which is specific to only bigport 4age's if i recall correctly
throw away that socket and buy a new nut
if you tip the gearbox oil will spill out where the yoke goes. just drain it and refill with 1.7L of oil
hope this helps. im sure one of the tech wizards will answer more questions in greater detail soon, but thankyou for actually going to the effort of putting up detailed pics