The port in the head should be left alone unless you take the head off. It leads directlt to the exhaust port for heat to come up and warm the intake and carb up quickly for cold weather driving.
The upsidedown U shape is not to be covered by anything except may the gasket. IF the gasket does not cover it, do not worry about it. It's just basicly a cave with no exhaust gas coming out of it.
The holes in the intake are in and out ports that connect to that port in the head. Ethier get a used EGR valve and gasket and install it, but do not hook it up. If you put a vacuum line to it, it'll work. No vacuum, it stays closed.
OR
Tap it for plugs which you can get at a hardware store.
ALSO, FYI, the EGR gasket material must be a special high temp gasket or it will just burn up. A factory part should be available at a dealer or possiblely on line for purchase.
(Guess how I know that one, LOL! )
To clean the head surface without head removal and to keep a clean engine free from debrise, lay down some rags in the engines valley covering up as much as possible and remove the rags very darefullly making dead sure nothing falls down into the pan.
Use a vacuum/shop vac to clean the rest up very very carefullly since even a vacuum will cause debrise to fly about and possibly fall into the engine.
*I THINK* the metal things are the tabs on the head gasket. There located where the head meets the block on the ends only on both sides? Then these metal tabs help hold the cork end gaskets in place.
IF you want to use end gaskets, just make sure they lay in nicely and do not squirm around when you put the intake on and tighten it up. Lay down a generous amount of sealent at the outter edge in the corners so oil dosen't spit out when runing the engine down the Hwy. at speed.
OH yea, now is a great time for a cam!
