I think one of theose nipples goes to the inlet air for the PCV system on the drivers valve cover and the other one comes from the valve, could be wrong, it's been awhile since I work in the 2.9.

The vacumm line to the air filter is for the warm air valve, I would check the system for a vacuum leak and put it back in the correct locations.

Overall I would work on pulling the codes and not disconnecting things, just MHO.