ok, after seeing those pictures, i can tell you what those 3 plugs are for. the 3 pin grey one is for the DPFE, the green one is for the knock sensor, the black one is for the EGR solenoid. so, dont worry about the grey and black one, but get the green one hooked up to the knock sensor if possible.
That little grey vacuum line goes to either the EVAP purge solenoid or the HVAC system both of which need a source of vacuum to work properly. in either case though, its not pulling a vacuum on the PCV valve(s). you need to delete the black box under the lower intake manifold (PM blackcoug as im sure he has several blockoff plates sitting around) and then run a large single line from the rear valve cover directly to the intake manifold (probably to the large port on the bottom).
the fuel block is an aftermarket piece designed to allow the hookup of the return style fuel system to the 3L returnless fuel rail. there really isnt much you can do with it other than make sure its sitting in a place that wont let it move around a lot.
the pipe behind the motor is probably the EVAP purge line. IIRC it should have a corrugated type hose that goes to the EVAP purge solenoid mounted on the firewall (which i bet isnt there). there should then be another corrugated type hose that leads from the solenoid to the the intake manifold.
BTW, if you ever decide that you are completely lost let me know and I can come up there one day (during the week or on the weekend) and help you figure out what you need to do. I live about an hour down I71 from Cincinnati and know these cars quite well. I could even bring some spare parts if needed (I have a stock 3L TB).