Cleaning up the engine bay?

[aseaman92]

I have a 93 240sx hatchback with a ka24de. I'm currently taking the engine out to rebuild but i don't know what need to hook back up or what i could get by without. for example the lower half of the intake manifold has a pipe that goes from exhaust to intake (something to do with emission control) do i need it or can i plug it.

Charcoal filter has four or five hoses that go across the fans guard witch i do not want be cause i am going to hook up electrical fan and i do not want to have that plastic or the hoses left in there.

One more thing there is a black plastic box in behind the intake box to the right of the strut tower there is a pipe coming from the exhaust manifold and snakes up to the box and there is one from the end of the intake where the filter is. I am wondering if you need it and what it is.