The TC rail will not work on an inline intake, so you will either have to upgrade to the box style intake or run the inline fuel rail. You will need to drill and tap the extra hole in the head for the box style intake as well. It looks like that turbo has no internal gate, so that means an E6 is out, you either need to source another turbo to use the E6 or source a different manifold with an external gate provision to use that turbo. As for the stuff on the side of the block, one is the oil cooler, the filter screws onto it. The other is the PCV breather, a vacuum line runs up from that to the pcv valve looks like it is missing though. As for accessories I am unsure, you can try and bolt them up and see what happens.
Its to bad it came all disassembled, your going to have a major headache finding the small pieces. When I get my car out of storage I will take a bunch of pictures of possible trouble areas and how everything is put together to help you out.