Nice motor! That turbo looks like a Holset..........excellent turbo!
2nd pic:
That's your turbo oil feed line. It's gonna be long 'cause it has to reach the turbo. Is the loop necessary? I don't think it'll cause any problems. Here's a pic of mine. It's the braided stainless steel line.
Turbo oil feed line
3rd pic:
Use that threaded hole for your aftermarket water temp gauge bulb. That was the hole for the factory W/T gauge. This is what I used for my oil distribution. The 90* at the top is for turbo oil feed and the straight shot out the end is for the aftermarket oil pressure gauge line.
Oil distribution
4th pic:
You should have a large vac tube on the underside of the upper intake. That connects to your PCV. The large vac tube up topside goes to your vac tree and supplies main engine vacuum. I used the smaller hose to provide vacuum to my AFPR. Also, a hose needs to go to the manifold for fuel vapor recovery from the charcoal canister (smog requirements).
5th pic:
As b_chandler stated, a line goes from your thermostat housing to the heater core inlet, the one closest to the pass side.
Heater inlet Heater inlet 2
6th pic:
As stated, that's your wastegate. Possibly a Tial. Quality wastegate! A vac line goes from the wastegate to a fitting on the turbo, just before the turbo outlet.
Hope this helped.