Big YES, you need to keep those parts you are asking if need to go back on. That's the Fuel Pressure Regulator and Fuel Damper. Those 2 items need to be replaced as the black color indicates they are the old style and may not be working properly and/or can leak. While you have the intake off, delete all of those coolant hoses and do the bypass. You will thank yourself later as one day one will blow and it may all have to come apart again to change a $.02 hose. Also, change all fuel hoses while it's apart and use good hose clamps or it will seep fuel. The PCV valves are cheap so replace them while they are out. Test the solenoids on the back of the plenum to ensure they are actually working (IACV unit) and the Aux. Air valve. You may want to disassembly them while they are easy to get at. The AAC has a lot do do with proper idle etc, and the Aux air gives you high idle for warm up.
Yes, love or hate the Z, there's nothing like it when it's performing properly.
